Starting phenix.real_space_refine on Sun Feb 25 20:15:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otc_13058/02_2024/7otc_13058_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Zn 2 6.06 5 P 4561 5.49 5 Mg 292 5.21 5 S 171 5.16 5 C 74353 2.51 5 N 27346 2.21 5 O 40407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 192": "OD1" <-> "OD2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "e PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "f PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h GLU 91": "OE1" <-> "OE2" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 107": "OD1" <-> "OD2" Residue "k PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n ASP 54": "OD1" <-> "OD2" Residue "n PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 55": "OD1" <-> "OD2" Residue "q ASP 15": "OD1" <-> "OD2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J ASP 49": "OD1" <-> "OD2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 35": "OD1" <-> "OD2" Residue "5 ASP 58": "OD1" <-> "OD2" Residue "5 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 36": "OE1" <-> "OE2" Residue "1 GLU 51": "OE1" <-> "OE2" Residue "w PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 98": "OE1" <-> "OE2" Residue "w ASP 206": "OD1" <-> "OD2" Residue "w ASP 258": "OD1" <-> "OD2" Residue "w GLU 452": "OE1" <-> "OE2" Residue "w ASP 521": "OD1" <-> "OD2" Residue "w TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147132 Number of models: 1 Model: "" Number of chains: 64 Chain: "a" Number of atoms: 32907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32907 Classifications: {'RNA': 1533} Modifications used: {'rna2p': 1, 'rna2p_pur': 115, 'rna2p_pyr': 88, 'rna3p': 9, 'rna3p_pur': 754, 'rna3p_pyr': 566} Link IDs: {'rna2p': 204, 'rna3p': 1328} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "f" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "g" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1236 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "h" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Conformer: "B" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} bond proxies already assigned to first conformer: 793 Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 555 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "s" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "t" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "A" Number of atoms: 62334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62334 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 150, 'rna3p': 18, 'rna3p_pur': 1386, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 435, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "C" Number of atoms: 2090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Conformer: "B" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} bond proxies already assigned to first conformer: 2112 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Conformer: "B" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} bond proxies already assigned to first conformer: 1140 Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} bond proxies already assigned to first conformer: 1050 Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 721 Classifications: {'peptide': 94} Link IDs: {'TRANS': 93} Chain breaks: 1 Chain: "V" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "X" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "5" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 529 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Conformer: "B" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} bond proxies already assigned to first conformer: 502 Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "w" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5196 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Unusual residues: {' MG': 61} Classifications: {'undetermined': 61} Link IDs: {None: 60} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 318 Unusual residues: {' MG': 219, 'ATP': 1, 'PUT': 8, 'SPD': 2} Classifications: {'undetermined': 230} Link IDs: {None: 229} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, '1I7': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0U3O SG CYS 5 16 62.537 67.380 129.827 1.00 56.13 S ATOM A0U40 SG CYS 5 18 61.266 64.888 132.202 1.00 55.98 S ATOM A0U7Y SG CYS 5 37 61.603 69.062 133.293 1.00 59.36 S ATOM A0U8J SG CYS 5 40 64.674 67.582 132.603 1.00 57.77 S ATOM A0VTI SG CYS 4 11 121.885 150.423 174.308 1.00 45.01 S ATOM A0VU7 SG CYS 4 14 120.382 153.495 172.492 1.00 40.96 S ATOM A0VX2 SG CYS 4 27 124.167 153.405 173.991 1.00 42.60 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG j 45 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG j 45 " occ=0.50 residue: pdb=" N AASN C 70 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 70 " occ=0.50 residue: pdb=" N AHIS J 80 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS J 80 " occ=0.50 residue: pdb=" N AARG L 78 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG L 78 " occ=0.50 residue: pdb=" N ALYS 3 23 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS 3 23 " occ=0.50 Time building chain proxies: 58.00, per 1000 atoms: 0.39 Number of scatterers: 147132 At special positions: 0 Unit cell: (266.664, 275.336, 221.136, 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 2 29.99 S 171 16.00 P 4561 15.00 Mg 292 11.99 O 40407 8.00 N 27346 7.00 C 74353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.36 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb=" ZN 5 301 " pdb="ZN ZN 5 301 " - pdb=" SG CYS 5 18 " pdb="ZN ZN 5 301 " - pdb=" SG CYS 5 37 " pdb="ZN ZN 5 301 " - pdb=" SG CYS 5 16 " pdb="ZN ZN 5 301 " - pdb=" SG CYS 5 40 " Number of angles added : 9 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11468 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 186 helices and 79 sheets defined 38.5% alpha, 20.7% beta 1440 base pairs and 2459 stacking pairs defined. Time for finding SS restraints: 76.49 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.735A pdb=" N MET b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 64 Proline residue: b 48 - end of helix removed outlier: 3.634A pdb=" N ARG b 63 " --> pdb=" O LYS b 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.539A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 121 removed outlier: 3.522A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR b 119 " --> pdb=" O LYS b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 6.777A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 229 Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.505A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.508A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.072A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 removed outlier: 3.509A pdb=" N LEU c 124 " --> pdb=" O ILE c 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU c 125 " --> pdb=" O THR c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.596A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.412A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.955A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.328A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.929A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU d 160 " --> pdb=" O LYS d 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 6.755A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.250A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU d 202 " --> pdb=" O HIS d 198 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 44 removed outlier: 4.753A pdb=" N ALA d 43 " --> pdb=" O GLN d 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.600A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 119 Processing helix chain 'e' and resid 132 through 148 removed outlier: 3.543A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.202A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.703A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 4.318A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU f 74 " --> pdb=" O VAL f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 106 Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.303A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.953A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.019A pdb=" N ALA g 61 " --> pdb=" O SER g 57 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.824A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 150 removed outlier: 4.416A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 removed outlier: 3.530A pdb=" N GLN h 118 " --> pdb=" O ARG h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.977A pdb=" N GLY i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 56 removed outlier: 4.216A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 4.609A pdb=" N LEU i 54 " --> pdb=" O GLN i 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.544A pdb=" N GLU i 89 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 4.065A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.963A pdb=" N VAL j 26 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU j 27 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 46 through 51 Processing helix chain 'k' and resid 54 through 60 removed outlier: 3.872A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 61 through 76 removed outlier: 3.783A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG k 69 " --> pdb=" O VAL k 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.590A pdb=" N THR k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.650A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.211A pdb=" N ALA m 18 " --> pdb=" O HIS m 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.720A pdb=" N ASP m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR m 55 " --> pdb=" O GLY m 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP m 58 " --> pdb=" O ASP m 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.068A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 24 through 35 removed outlier: 6.319A pdb=" N ASN n 35 " --> pdb=" O ILE n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 6.391A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 3.849A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.504A pdb=" N SER o 13 " --> pdb=" O ALA o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.064A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.763A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.801A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 Processing helix chain 'r' and resid 11 through 17 removed outlier: 4.164A pdb=" N ALA r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU r 16 " --> pdb=" O ARG r 12 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY r 17 " --> pdb=" O PHE r 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 11 through 17' Processing helix chain 'r' and resid 25 through 34 removed outlier: 5.296A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.777A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN r 54 " --> pdb=" O LYS r 50 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 Processing helix chain 't' and resid 4 through 42 removed outlier: 3.921A pdb=" N PHE t 31 " --> pdb=" O MET t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix removed outlier: 3.562A pdb=" N ASP t 59 " --> pdb=" O GLN t 55 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 38 removed outlier: 4.393A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR u 38 " --> pdb=" O ARG u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 69 removed outlier: 3.529A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG u 69 " --> pdb=" O ALA u 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.534A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.853A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.646A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 3.512A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 6.041A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.693A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.304A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.613A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.749A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.278A pdb=" N TYR F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.620A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.299A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.536A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.660A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 4.326A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 4.237A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.657A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.145A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.457A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.932A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.787A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.591A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.618A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.113A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.663A pdb=" N LEU L 82 " --> pdb=" O AARG L 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.798A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.008A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.387A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.589A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.739A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 3.607A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.040A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.624A pdb=" N GLU O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.319A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.666A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.824A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.745A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.737A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.883A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.722A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.620A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.674A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 6.108A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.414A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.957A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.606A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.763A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.588A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 2 through 9' Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.715A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.204A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain '5' and resid 49 through 54 removed outlier: 4.516A pdb=" N THR 5 53 " --> pdb=" O ARG 5 49 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY 5 54 " --> pdb=" O ASP 5 50 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 49 through 54' Processing helix chain '5' and resid 55 through 65 Processing helix chain '0' and resid 9 through 19 removed outlier: 4.845A pdb=" N HIS 0 19 " --> pdb=" O MET 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.166A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.687A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 4.817A pdb=" N LYS 3 36 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA 3 37 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 Proline residue: 3 46 - end of helix Processing helix chain '3' and resid 51 through 63 removed outlier: 4.544A pdb=" N GLY 3 56 " --> pdb=" O LYS 3 52 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU 3 57 " --> pdb=" O GLY 3 53 " (cutoff:3.500A) Proline residue: 3 63 - end of helix Processing helix chain 'w' and resid 22 through 39 Processing helix chain 'w' and resid 95 through 107 removed outlier: 4.733A pdb=" N ASP w 107 " --> pdb=" O MET w 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 120 through 134 removed outlier: 3.560A pdb=" N ARG w 128 " --> pdb=" O GLU w 124 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN w 129 " --> pdb=" O THR w 125 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA w 130 " --> pdb=" O VAL w 126 " (cutoff:3.500A) Processing helix chain 'w' and resid 150 through 162 Processing helix chain 'w' and resid 208 through 231 removed outlier: 4.476A pdb=" N GLU w 213 " --> pdb=" O ALA w 209 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU w 214 " --> pdb=" O ASP w 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA w 229 " --> pdb=" O SER w 225 " (cutoff:3.500A) Processing helix chain 'w' and resid 232 through 240 removed outlier: 3.630A pdb=" N LYS w 236 " --> pdb=" O GLU w 232 " (cutoff:3.500A) Processing helix chain 'w' and resid 244 through 259 Processing helix chain 'w' and resid 274 through 285 Processing helix chain 'w' and resid 288 through 293 Proline residue: w 293 - end of helix Processing helix chain 'w' and resid 426 through 443 removed outlier: 4.321A pdb=" N LYS w 430 " --> pdb=" O ALA w 426 " (cutoff:3.500A) Proline residue: w 443 - end of helix Processing helix chain 'w' and resid 462 through 476 Processing helix chain 'w' and resid 526 through 531 removed outlier: 3.594A pdb=" N ASN w 530 " --> pdb=" O GLU w 526 " (cutoff:3.500A) Proline residue: w 531 - end of helix No H-bonds generated for 'chain 'w' and resid 526 through 531' Processing helix chain 'w' and resid 549 through 564 removed outlier: 4.282A pdb=" N GLY w 564 " --> pdb=" O GLN w 560 " (cutoff:3.500A) Processing helix chain 'w' and resid 589 through 609 removed outlier: 3.514A pdb=" N LYS w 609 " --> pdb=" O PHE w 605 " (cutoff:3.500A) Processing helix chain 'w' and resid 624 through 639 removed outlier: 5.165A pdb=" N GLY w 629 " --> pdb=" O GLU w 625 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP w 630 " --> pdb=" O GLU w 626 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG w 639 " --> pdb=" O LEU w 635 " (cutoff:3.500A) Processing helix chain 'w' and resid 659 through 664 removed outlier: 4.549A pdb=" N PHE w 664 " --> pdb=" O LEU w 660 " (cutoff:3.500A) Processing helix chain 'w' and resid 665 through 675 removed outlier: 3.514A pdb=" N SER w 672 " --> pdb=" O THR w 668 " (cutoff:3.500A) Processing helix chain 'w' and resid 691 through 700 Processing sheet with id= 1, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.350A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 90 through 93 removed outlier: 3.728A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'c' and resid 164 through 169 removed outlier: 5.976A pdb=" N ARG c 164 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.868A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.756A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.855A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 33 through 41 removed outlier: 6.767A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.567A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'f' and resid 43 through 47 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.127A pdb=" N THR g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.569A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.982A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'i' and resid 5 through 11 removed outlier: 3.668A pdb=" N LYS i 27 " --> pdb=" O LEU i 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.298A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER j 101 " --> pdb=" O ARG j 7 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG j 9 " --> pdb=" O GLN j 99 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'k' and resid 42 through 45 removed outlier: 4.077A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY k 19 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL k 84 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA k 21 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL k 86 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE k 23 " --> pdb=" O VAL k 86 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY k 88 " --> pdb=" O ILE k 23 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA k 25 " --> pdb=" O GLY k 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU k 82 " --> pdb=" O ARG k 106 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.046A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY l 85 " --> pdb=" O ARG l 94 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG l 94 " --> pdb=" O GLY l 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.135A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'p' and resid 4 through 10 removed outlier: 3.777A pdb=" N HIS p 9 " --> pdb=" O PHE p 16 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'q' and resid 37 through 48 removed outlier: 6.957A pdb=" N VAL q 22 " --> pdb=" O VAL q 13 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU q 26 " --> pdb=" O GLN q 9 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLN q 9 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 13.927A pdb=" N PHE q 28 " --> pdb=" O THR q 7 " (cutoff:3.500A) removed outlier: 17.000A pdb=" N THR q 7 " --> pdb=" O PHE q 28 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 's' and resid 30 through 34 removed outlier: 3.587A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 25, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.624A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.002A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.869A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= 30, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.650A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.506A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.600A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.665A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 1 through 5 removed outlier: 6.031A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.894A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.640A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 155 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 15 through 20 removed outlier: 6.402A pdb=" N GLN G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 39, first strand: chain 'G' and resid 94 through 99 removed outlier: 7.090A pdb=" N ASN G 101 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.937A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.796A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.622A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.213A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'K' and resid 39 through 42 Processing sheet with id= 45, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.549A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.697A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.298A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.906A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.309A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.518A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.932A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 17 through 22 removed outlier: 4.437A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 55, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 56, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.313A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 1 through 8 removed outlier: 5.858A pdb=" N MET S 1 " --> pdb=" O ASP S 109 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP S 109 " --> pdb=" O MET S 1 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.363A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'U' and resid 40 through 46 removed outlier: 5.444A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 61, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.631A pdb=" N ILE V 63 " --> pdb=" O ILE V 70 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL V 72 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.312A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 64, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.512A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'X' and resid 34 through 41 Processing sheet with id= 66, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.319A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '5' and resid 20 through 25 removed outlier: 4.003A pdb=" N ASN 5 20 " --> pdb=" O CYS 5 16 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE 5 24 " --> pdb=" O ILE 5 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 5 32 " --> pdb=" O THR 5 13 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1' and resid 20 through 24 removed outlier: 6.790A pdb=" N ILE 1 48 " --> pdb=" O SER 1 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU 1 51 " --> pdb=" O LEU 1 34 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU 1 34 " --> pdb=" O GLU 1 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '3' and resid 22 through 25 removed outlier: 5.813A pdb=" N PHE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '4' and resid 1 through 5 removed outlier: 6.798A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'w' and resid 67 through 73 removed outlier: 7.463A pdb=" N ARG w 9 " --> pdb=" O PRO w 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG w 83 " --> pdb=" O ARG w 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE w 15 " --> pdb=" O ILE w 87 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA w 17 " --> pdb=" O THR w 89 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER w 16 " --> pdb=" O VAL w 110 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU w 263 " --> pdb=" O ARG w 137 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL w 167 " --> pdb=" O ILE w 262 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL w 264 " --> pdb=" O VAL w 167 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS w 266 " --> pdb=" O LEU w 169 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'w' and resid 170 through 173 removed outlier: 3.638A pdb=" N GLY w 181 " --> pdb=" O ILE w 173 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'w' and resid 324 through 327 removed outlier: 7.972A pdb=" N PHE w 317 " --> pdb=" O ASP w 399 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP w 399 " --> pdb=" O PHE w 317 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP w 395 " --> pdb=" O ALA w 321 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR w 396 " --> pdb=" O SER w 352 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'w' and resid 362 through 365 removed outlier: 4.281A pdb=" N ARG w 362 " --> pdb=" O ILE w 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE w 386 " --> pdb=" O ARG w 362 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'w' and resid 445 through 450 removed outlier: 3.818A pdb=" N GLN w 455 " --> pdb=" O ASP w 450 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR w 456 " --> pdb=" O VAL w 420 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N SER w 417 " --> pdb=" O PRO w 486 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'w' and resid 500 through 510 removed outlier: 3.999A pdb=" N GLN w 514 " --> pdb=" O LYS w 507 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER w 509 " --> pdb=" O ARG w 512 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG w 512 " --> pdb=" O SER w 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU w 535 " --> pdb=" O MET w 574 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE w 576 " --> pdb=" O GLU w 535 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE w 537 " --> pdb=" O ILE w 576 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'w' and resid 644 through 648 removed outlier: 3.913A pdb=" N GLY w 644 " --> pdb=" O HIS w 655 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY w 651 " --> pdb=" O GLU w 648 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER w 679 " --> pdb=" O GLU w 622 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'w' and resid 490 through 494 removed outlier: 5.931A pdb=" N LEU w 613 " --> pdb=" O ARG w 491 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'w' and resid 515 through 519 removed outlier: 6.085A pdb=" N TYR w 515 " --> pdb=" O HIS w 584 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS w 584 " --> pdb=" O TYR w 515 " (cutoff:3.500A) 2111 hydrogen bonds defined for protein. 6217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3578 hydrogen bonds 5634 hydrogen bond angles 0 basepair planarities 1440 basepair parallelities 2459 stacking parallelities Total time for adding SS restraints: 241.79 Time building geometry restraints manager: 66.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 12298 1.28 - 1.41: 51207 1.41 - 1.54: 86253 1.54 - 1.68: 9209 1.68 - 1.81: 306 Bond restraints: 159273 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.520 0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.520 0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" N3 5MU A 747 " pdb=" C4 5MU A 747 " ideal model delta sigma weight residual 1.182 1.414 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" N3 5MU A1939 " pdb=" C4 5MU A1939 " ideal model delta sigma weight residual 1.182 1.413 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ATP A3001 " pdb=" C4' ATP A3001 " ideal model delta sigma weight residual 1.305 1.524 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 159268 not shown) Histogram of bond angle deviations from ideal: 88.62 - 98.92: 59 98.92 - 109.22: 62161 109.22 - 119.52: 101975 119.52 - 129.83: 70555 129.83 - 140.13: 2851 Bond angle restraints: 237601 Sorted by residual: angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C8 G7M a 527 " ideal model delta sigma weight residual 94.96 132.17 -37.21 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " pdb=" C8 G7M A2069 " ideal model delta sigma weight residual 94.96 131.46 -36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C1' ATP A3001 " pdb=" N9 ATP A3001 " pdb=" C8 ATP A3001 " ideal model delta sigma weight residual 92.72 127.14 -34.42 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ARG b 21 " pdb=" CG ARG b 21 " pdb=" CD ARG b 21 " ideal model delta sigma weight residual 111.30 88.79 22.51 2.30e+00 1.89e-01 9.58e+01 angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C4 G7M a 527 " ideal model delta sigma weight residual 142.80 116.64 26.16 3.00e+00 1.11e-01 7.60e+01 ... (remaining 237596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 89905 35.82 - 71.65: 10575 71.65 - 107.47: 1223 107.47 - 143.30: 22 143.30 - 179.12: 10 Dihedral angle restraints: 101735 sinusoidal: 83942 harmonic: 17793 Sorted by residual: dihedral pdb=" CA VAL R 51 " pdb=" C VAL R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual -180.00 -130.32 -49.68 0 5.00e+00 4.00e-02 9.87e+01 dihedral pdb=" O4' C a 330 " pdb=" C1' C a 330 " pdb=" N1 C a 330 " pdb=" C2 C a 330 " ideal model delta sinusoidal sigma weight residual -160.00 4.98 -164.98 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' C a1109 " pdb=" C1' C a1109 " pdb=" N1 C a1109 " pdb=" C2 C a1109 " ideal model delta sinusoidal sigma weight residual -160.00 0.39 -160.39 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 101732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 29091 0.085 - 0.170: 975 0.170 - 0.255: 65 0.255 - 0.340: 2 0.340 - 0.425: 3 Chirality restraints: 30136 Sorted by residual: chirality pdb=" CG LEU b 129 " pdb=" CB LEU b 129 " pdb=" CD1 LEU b 129 " pdb=" CD2 LEU b 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB ILE w 261 " pdb=" CA ILE w 261 " pdb=" CG1 ILE w 261 " pdb=" CG2 ILE w 261 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CG LEU w 106 " pdb=" CB LEU w 106 " pdb=" CD1 LEU w 106 " pdb=" CD2 LEU w 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 30133 not shown) Planarity restraints: 13179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.054 2.00e-02 2.50e+03 5.98e-01 8.06e+03 pdb=" C4' 5MC a1407 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.636 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.638 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.183 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.968 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.219 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.036 2.00e-02 2.50e+03 5.93e-01 7.91e+03 pdb=" C4' OMG A2251 " 0.448 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.696 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.593 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.212 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 0.922 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.210 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1835 " 0.041 2.00e-02 2.50e+03 5.88e-01 7.77e+03 pdb=" C4' 2MG A1835 " 0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG A1835 " 0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG A1835 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1835 " -0.576 2.00e-02 2.50e+03 pdb=" C2' 2MG A1835 " -0.214 2.00e-02 2.50e+03 pdb=" O2' 2MG A1835 " 0.910 2.00e-02 2.50e+03 pdb=" C1' 2MG A1835 " 0.215 2.00e-02 2.50e+03 pdb=" N9 2MG A1835 " -0.911 2.00e-02 2.50e+03 ... (remaining 13176 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 832 2.46 - 3.07: 87733 3.07 - 3.68: 276324 3.68 - 4.29: 431870 4.29 - 4.90: 572462 Nonbonded interactions: 1369221 Sorted by model distance: nonbonded pdb=" O2' G a 830 " pdb=" NH1 ARG b 21 " model vdw 1.846 2.520 nonbonded pdb=" OP2 C a 980 " pdb="MG MG a1619 " model vdw 1.895 2.170 nonbonded pdb=" O6 G a1222 " pdb="MG MG a1619 " model vdw 1.916 2.170 nonbonded pdb=" O6 G A 570 " pdb="MG MG A3027 " model vdw 1.938 2.170 nonbonded pdb=" OP1 C A2006 " pdb="MG MG A3075 " model vdw 1.949 2.170 ... (remaining 1369216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 15.840 Check model and map are aligned: 1.640 Set scattering table: 1.030 Process input model: 570.110 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 608.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.005 0.282 159273 Z= 0.332 Angle : 0.715 37.208 237601 Z= 0.360 Chirality : 0.035 0.425 30136 Planarity : 0.018 0.598 13179 Dihedral : 22.633 179.124 90267 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.59 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 0.78 % Favored : 99.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.49 (0.10), residues: 6145 helix: 0.52 (0.11), residues: 2025 sheet: -0.52 (0.14), residues: 1244 loop : -0.75 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP w 193 HIS 0.027 0.002 HIS f 3 PHE 0.030 0.002 PHE i 20 TYR 0.040 0.002 TYR w 285 ARG 0.027 0.001 ARG c 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1261 time to evaluate : 6.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 170 TRP cc_start: 0.6139 (p90) cc_final: 0.5903 (p90) REVERT: e 128 TYR cc_start: 0.8818 (m-80) cc_final: 0.8488 (m-80) REVERT: k 100 LEU cc_start: 0.7726 (tt) cc_final: 0.7451 (mp) REVERT: l 61 PHE cc_start: 0.7963 (m-10) cc_final: 0.7683 (m-10) REVERT: C 191 THR cc_start: 0.8997 (m) cc_final: 0.8757 (m) REVERT: K 18 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7885 (tpt-90) REVERT: M 71 LYS cc_start: 0.8339 (tttp) cc_final: 0.8083 (tttt) REVERT: M 73 ILE cc_start: 0.8926 (mm) cc_final: 0.8708 (mp) REVERT: N 110 MET cc_start: 0.7647 (mmm) cc_final: 0.7414 (mmm) REVERT: P 11 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6810 (mt-10) REVERT: 1 6 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7963 (mtp-110) REVERT: w 343 VAL cc_start: 0.5504 (p) cc_final: 0.5001 (p) REVERT: w 467 ASP cc_start: 0.7235 (t0) cc_final: 0.7028 (t70) REVERT: w 500 ASP cc_start: 0.6894 (m-30) cc_final: 0.6578 (m-30) REVERT: w 657 GLU cc_start: 0.6664 (mp0) cc_final: 0.6376 (mp0) outliers start: 2 outliers final: 3 residues processed: 1263 average time/residue: 2.3700 time to fit residues: 4171.8864 Evaluate side-chains 971 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 968 time to evaluate : 6.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain F residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 891 optimal weight: 1.9990 chunk 800 optimal weight: 0.0570 chunk 444 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 539 optimal weight: 20.0000 chunk 427 optimal weight: 10.0000 chunk 827 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 503 optimal weight: 8.9990 chunk 616 optimal weight: 30.0000 chunk 958 optimal weight: 5.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 HIS ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN e 19 ASN g 153 HIS h 4 GLN i 31 ASN i 32 GLN j 4 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS k 28 ASN k 64 GLN ** k 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN p 40 ASN q 31 HIS r 54 GLN s 57 HIS t 70 ASN C 115 GLN C 134 ASN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN O 100 HIS P 12 GLN Q 37 GLN Q 59 GLN Q 71 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 150 ASN w 198 GLN w 220 GLN ** w 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 159273 Z= 0.393 Angle : 0.734 21.154 237601 Z= 0.381 Chirality : 0.043 0.397 30136 Planarity : 0.007 0.145 13179 Dihedral : 23.038 176.565 78007 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 3.44 % Allowed : 14.54 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.32 (0.10), residues: 6145 helix: 0.63 (0.11), residues: 2040 sheet: -0.38 (0.14), residues: 1255 loop : -0.66 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP g 103 HIS 0.014 0.002 HIS j 15 PHE 0.018 0.002 PHE R 93 TYR 0.034 0.002 TYR F 143 ARG 0.016 0.001 ARG t 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1000 time to evaluate : 6.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 35 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6294 (ppt-90) REVERT: d 8 LYS cc_start: 0.8013 (tppt) cc_final: 0.7782 (tppt) REVERT: d 154 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7623 (ptt-90) REVERT: e 128 TYR cc_start: 0.8875 (m-80) cc_final: 0.8625 (m-80) REVERT: f 90 MET cc_start: 0.7196 (ttt) cc_final: 0.6669 (ttt) REVERT: g 92 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6221 (pmt170) REVERT: l 30 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8194 (mptp) REVERT: l 94 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5618 (mtp85) REVERT: m 70 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7541 (tpp-160) REVERT: o 62 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: t 24 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7673 (mmt90) REVERT: C 163 GLN cc_start: 0.8230 (tt0) cc_final: 0.7890 (tt0) REVERT: C 251 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: J 31 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6526 (mm-30) REVERT: N 64 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8079 (mtt90) REVERT: P 29 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7060 (mmmt) REVERT: Q 109 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8708 (mp) REVERT: R 97 LYS cc_start: 0.8038 (tttm) cc_final: 0.7820 (tttm) REVERT: V 70 ILE cc_start: 0.7746 (mt) cc_final: 0.7496 (mt) REVERT: W 14 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8482 (mtm-85) REVERT: 1 6 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8216 (mtp-110) REVERT: w 467 ASP cc_start: 0.7107 (t0) cc_final: 0.6876 (t0) REVERT: w 641 MET cc_start: 0.6340 (pp-130) cc_final: 0.5571 (ppp) outliers start: 176 outliers final: 73 residues processed: 1078 average time/residue: 2.2714 time to fit residues: 3458.3239 Evaluate side-chains 1008 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 923 time to evaluate : 6.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 35 ARG Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 64 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 62 GLN Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 24 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain w residue 105 VAL Chi-restraints excluded: chain w residue 125 THR Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 590 GLU Chi-restraints excluded: chain w residue 618 LYS Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Chi-restraints excluded: chain w residue 685 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 532 optimal weight: 10.0000 chunk 297 optimal weight: 0.0040 chunk 798 optimal weight: 4.9990 chunk 652 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 960 optimal weight: 7.9990 chunk 1037 optimal weight: 9.9990 chunk 855 optimal weight: 9.9990 chunk 952 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 770 optimal weight: 9.9990 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN d 152 GLN e 19 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN i 50 GLN j 4 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS k 28 ASN ** k 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN r 52 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN C 115 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN P 12 GLN P 75 GLN Q 59 GLN Q 71 GLN R 6 GLN S 31 GLN S 57 ASN T 59 ASN Z 9 GLN 0 42 HIS w 198 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 159273 Z= 0.443 Angle : 0.766 17.552 237601 Z= 0.396 Chirality : 0.044 0.349 30136 Planarity : 0.008 0.147 13179 Dihedral : 22.959 176.382 78002 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 5.58 % Allowed : 17.52 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.54 (0.10), residues: 6145 helix: 0.38 (0.11), residues: 2035 sheet: -0.40 (0.14), residues: 1226 loop : -0.79 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP w 448 HIS 0.010 0.002 HIS V 88 PHE 0.035 0.002 PHE w 322 TYR 0.024 0.002 TYR w 687 ARG 0.013 0.001 ARG f 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 994 time to evaluate : 5.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.7589 (mmt) cc_final: 0.7304 (mmt) REVERT: b 35 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6405 (ppt-90) REVERT: d 8 LYS cc_start: 0.7813 (tppt) cc_final: 0.7561 (tppt) REVERT: d 154 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7670 (ptt-90) REVERT: f 102 MET cc_start: 0.3142 (OUTLIER) cc_final: 0.2254 (pmt) REVERT: l 30 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8258 (mptp) REVERT: l 44 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8180 (mmtt) REVERT: l 94 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5841 (mtp85) REVERT: o 62 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: o 77 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7112 (ptm160) REVERT: q 12 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8094 (t) REVERT: s 41 PHE cc_start: 0.8398 (m-10) cc_final: 0.8045 (m-10) REVERT: t 24 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7632 (mmt90) REVERT: u 31 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5159 (mp0) REVERT: C 132 MET cc_start: 0.8011 (mtm) cc_final: 0.7750 (mtm) REVERT: C 189 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7746 (mtt180) REVERT: C 225 MET cc_start: 0.8827 (mtt) cc_final: 0.8377 (mtt) REVERT: C 251 GLN cc_start: 0.8195 (pp30) cc_final: 0.7992 (tm-30) REVERT: F 170 LEU cc_start: 0.6673 (pp) cc_final: 0.6211 (tm) REVERT: G 104 ASN cc_start: 0.6887 (m110) cc_final: 0.6509 (m110) REVERT: K 7 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7084 (mmm) REVERT: K 49 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7174 (mpp-170) REVERT: K 51 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8281 (mttp) REVERT: K 88 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8284 (t0) REVERT: L 123 ARG cc_start: 0.7241 (ptp-110) cc_final: 0.6976 (ptp-110) REVERT: N 64 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8029 (mtt90) REVERT: P 29 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7038 (mmmt) REVERT: P 98 TYR cc_start: 0.8817 (m-10) cc_final: 0.8552 (m-10) REVERT: U 17 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8007 (pttp) REVERT: V 70 ILE cc_start: 0.7633 (mt) cc_final: 0.7374 (mt) REVERT: X 25 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8193 (p) REVERT: Z 45 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7949 (mmt90) REVERT: 0 10 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8127 (mtt-85) REVERT: 1 6 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8265 (mtp-110) REVERT: 4 36 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (ttp80) REVERT: w 278 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5397 (ptp) REVERT: w 657 GLU cc_start: 0.6370 (mp0) cc_final: 0.6069 (mp0) REVERT: w 689 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6666 (mt-10) outliers start: 285 outliers final: 110 residues processed: 1144 average time/residue: 2.2466 time to fit residues: 3645.3132 Evaluate side-chains 1059 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 927 time to evaluate : 6.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 35 ARG Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 62 GLN Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 24 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 17 LYS Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 36 ARG Chi-restraints excluded: chain w residue 27 THR Chi-restraints excluded: chain w residue 125 THR Chi-restraints excluded: chain w residue 138 ILE Chi-restraints excluded: chain w residue 278 MET Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 455 GLN Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Chi-restraints excluded: chain w residue 689 GLU Chi-restraints excluded: chain w residue 694 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 949 optimal weight: 20.0000 chunk 722 optimal weight: 1.9990 chunk 498 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 458 optimal weight: 4.9990 chunk 645 optimal weight: 4.9990 chunk 964 optimal weight: 9.9990 chunk 1020 optimal weight: 0.4980 chunk 503 optimal weight: 5.9990 chunk 913 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 94 HIS b 103 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN e 19 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN j 4 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS k 28 ASN k 109 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN L 4 ASN O 104 GLN R 6 GLN S 57 ASN 4 35 GLN w 198 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 159273 Z= 0.275 Angle : 0.652 18.817 237601 Z= 0.346 Chirality : 0.038 0.367 30136 Planarity : 0.006 0.136 13179 Dihedral : 22.890 177.264 78002 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 4.78 % Allowed : 20.51 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.37 (0.10), residues: 6145 helix: 0.59 (0.11), residues: 2042 sheet: -0.34 (0.14), residues: 1203 loop : -0.73 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 103 HIS 0.007 0.001 HIS e 89 PHE 0.032 0.002 PHE b 50 TYR 0.026 0.002 TYR O 99 ARG 0.012 0.001 ARG w 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 976 time to evaluate : 6.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.7490 (mmt) cc_final: 0.7276 (mmt) REVERT: b 35 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6405 (ppt-90) REVERT: d 154 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7584 (ptt-90) REVERT: e 96 MET cc_start: 0.8384 (mtm) cc_final: 0.8162 (mtm) REVERT: e 147 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7769 (ttm) REVERT: f 102 MET cc_start: 0.3206 (OUTLIER) cc_final: 0.2274 (pmt) REVERT: g 7 ILE cc_start: 0.4006 (OUTLIER) cc_final: 0.3619 (pt) REVERT: h 27 MET cc_start: 0.7884 (ptp) cc_final: 0.7515 (ptt) REVERT: l 30 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8224 (mptp) REVERT: l 44 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8082 (mmtt) REVERT: l 94 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5755 (mtp85) REVERT: n 54 ASP cc_start: 0.7375 (t0) cc_final: 0.7110 (t0) REVERT: q 12 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7886 (t) REVERT: q 57 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7391 (p0) REVERT: r 61 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8039 (mtt-85) REVERT: s 41 PHE cc_start: 0.8463 (m-10) cc_final: 0.8123 (m-10) REVERT: t 76 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7471 (mtpt) REVERT: C 163 GLN cc_start: 0.8250 (tt0) cc_final: 0.7904 (tt0) REVERT: C 225 MET cc_start: 0.8847 (mtt) cc_final: 0.8405 (mtt) REVERT: D 168 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: E 144 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5604 (pp20) REVERT: E 145 ASP cc_start: 0.6681 (t70) cc_final: 0.6441 (t70) REVERT: K 7 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6996 (mmm) REVERT: K 92 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: L 4 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8672 (p0) REVERT: L 123 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6813 (ptp-110) REVERT: M 10 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7436 (mtm-85) REVERT: N 64 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8023 (mtt90) REVERT: P 29 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6944 (mmmt) REVERT: R 1 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7307 (ttp) REVERT: R 22 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8487 (pp) REVERT: R 48 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8235 (mtmm) REVERT: S 92 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7277 (ttm170) REVERT: V 70 ILE cc_start: 0.7735 (mt) cc_final: 0.7528 (mt) REVERT: 0 10 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7675 (mtt-85) REVERT: 1 6 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8217 (mtp-110) REVERT: w 101 ARG cc_start: 0.6049 (mmt90) cc_final: 0.5708 (mpt180) REVERT: w 278 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.5233 (ptp) REVERT: w 689 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6748 (mt-10) outliers start: 244 outliers final: 108 residues processed: 1096 average time/residue: 2.2396 time to fit residues: 3534.6432 Evaluate side-chains 1069 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 939 time to evaluate : 6.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 35 ARG Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 MET Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain w residue 27 THR Chi-restraints excluded: chain w residue 125 THR Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 278 MET Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain w residue 405 ILE Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Chi-restraints excluded: chain w residue 689 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 850 optimal weight: 8.9990 chunk 579 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 760 optimal weight: 0.5980 chunk 421 optimal weight: 30.0000 chunk 871 optimal weight: 0.0470 chunk 705 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 521 optimal weight: 10.0000 chunk 916 optimal weight: 0.8980 chunk 257 optimal weight: 0.0980 overall best weight: 1.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN d 152 GLN e 19 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 4 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN L 4 ASN O 104 GLN R 6 GLN S 57 ASN W 57 HIS ** w 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 198 GLN ** w 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 159273 Z= 0.159 Angle : 0.593 17.082 237601 Z= 0.318 Chirality : 0.034 0.380 30136 Planarity : 0.006 0.128 13179 Dihedral : 22.843 177.550 78002 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 4.25 % Allowed : 21.96 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.20 (0.10), residues: 6145 helix: 0.77 (0.11), residues: 2046 sheet: -0.24 (0.15), residues: 1188 loop : -0.66 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP w 193 HIS 0.011 0.001 HIS w 219 PHE 0.036 0.001 PHE w 322 TYR 0.026 0.001 TYR w 523 ARG 0.011 0.000 ARG s 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1030 time to evaluate : 6.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 35 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6371 (ppt-90) REVERT: e 96 MET cc_start: 0.8299 (mtm) cc_final: 0.8084 (mtm) REVERT: f 102 MET cc_start: 0.3089 (OUTLIER) cc_final: 0.2122 (pmt) REVERT: l 44 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8061 (mmtt) REVERT: q 57 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7130 (p0) REVERT: u 31 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5127 (mp0) REVERT: C 163 GLN cc_start: 0.8183 (tt0) cc_final: 0.7566 (tt0) REVERT: C 225 MET cc_start: 0.8787 (mtt) cc_final: 0.8363 (mtt) REVERT: D 168 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: E 144 GLU cc_start: 0.5925 (tm-30) cc_final: 0.5610 (pp20) REVERT: K 92 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: L 123 ARG cc_start: 0.7103 (ptp-110) cc_final: 0.6847 (ptp-110) REVERT: N 24 MET cc_start: 0.7994 (mtm) cc_final: 0.7731 (mtm) REVERT: P 29 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6973 (mmmt) REVERT: Q 20 GLN cc_start: 0.8286 (mt0) cc_final: 0.8072 (mt0) REVERT: R 22 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8446 (pp) REVERT: w 689 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6812 (mt-10) outliers start: 217 outliers final: 101 residues processed: 1137 average time/residue: 2.2219 time to fit residues: 3601.9373 Evaluate side-chains 1080 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 970 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 35 ARG Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 45 GLU Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain w residue 27 THR Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 279 LEU Chi-restraints excluded: chain w residue 282 VAL Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 405 ILE Chi-restraints excluded: chain w residue 406 LEU Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 455 GLN Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 649 VAL Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Chi-restraints excluded: chain w residue 689 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 343 optimal weight: 7.9990 chunk 919 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 599 optimal weight: 90.0000 chunk 251 optimal weight: 7.9990 chunk 1021 optimal weight: 30.0000 chunk 848 optimal weight: 6.9990 chunk 473 optimal weight: 80.0000 chunk 84 optimal weight: 20.0000 chunk 337 optimal weight: 2.9990 chunk 536 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN e 19 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 4 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN p 40 ASN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN C 239 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN J 67 ASN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Q 71 GLN R 6 GLN S 15 GLN S 57 ASN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 HIS 2 6 GLN w 198 GLN w 454 ASN w 560 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 159273 Z= 0.444 Angle : 0.751 17.102 237601 Z= 0.387 Chirality : 0.043 0.348 30136 Planarity : 0.007 0.146 13179 Dihedral : 22.840 176.442 78002 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 4.99 % Allowed : 22.78 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.39 (0.10), residues: 6145 helix: 0.60 (0.11), residues: 2038 sheet: -0.40 (0.14), residues: 1222 loop : -0.74 (0.11), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 80 HIS 0.009 0.002 HIS e 89 PHE 0.028 0.002 PHE b 50 TYR 0.023 0.002 TYR S 38 ARG 0.016 0.001 ARG w 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 983 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 8 LYS cc_start: 0.7677 (tppt) cc_final: 0.7421 (tppt) REVERT: d 154 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7381 (ptt180) REVERT: f 65 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7427 (tm-30) REVERT: f 102 MET cc_start: 0.3447 (OUTLIER) cc_final: 0.2464 (pmt) REVERT: i 18 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7458 (mtm110) REVERT: l 10 LYS cc_start: 0.7568 (tptt) cc_final: 0.7316 (pttt) REVERT: l 30 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8231 (mptp) REVERT: l 44 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8129 (mmtt) REVERT: l 94 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5821 (mtp85) REVERT: n 54 ASP cc_start: 0.7510 (t0) cc_final: 0.7264 (t0) REVERT: o 62 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: q 57 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7480 (p0) REVERT: t 49 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7537 (tttp) REVERT: u 31 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5102 (mp0) REVERT: C 163 GLN cc_start: 0.8263 (tt0) cc_final: 0.7871 (tt0) REVERT: C 225 MET cc_start: 0.8866 (mtt) cc_final: 0.8439 (mtt) REVERT: D 168 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: E 144 GLU cc_start: 0.5813 (tm-30) cc_final: 0.5485 (pp20) REVERT: J 31 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: J 93 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8462 (mm) REVERT: J 96 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6978 (tpt-90) REVERT: K 7 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6954 (mmm) REVERT: K 92 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: M 66 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6694 (mmm160) REVERT: M 114 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7629 (ttt-90) REVERT: N 8 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8189 (mtt90) REVERT: N 64 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: P 20 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8011 (p90) REVERT: P 29 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7075 (mmmt) REVERT: R 22 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8544 (pp) REVERT: S 92 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: X 22 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8611 (mt) REVERT: X 25 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8194 (p) REVERT: 0 10 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7790 (mtt-85) outliers start: 255 outliers final: 150 residues processed: 1120 average time/residue: 2.2497 time to fit residues: 3592.4597 Evaluate side-chains 1134 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 959 time to evaluate : 6.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 62 GLN Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 45 GLU Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 49 LYS Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain w residue 16 SER Chi-restraints excluded: chain w residue 27 THR Chi-restraints excluded: chain w residue 125 THR Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 449 THR Chi-restraints excluded: chain w residue 590 GLU Chi-restraints excluded: chain w residue 623 THR Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 649 VAL Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 985 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 582 optimal weight: 4.9990 chunk 746 optimal weight: 10.0000 chunk 578 optimal weight: 4.9990 chunk 860 optimal weight: 6.9990 chunk 570 optimal weight: 10.0000 chunk 1017 optimal weight: 50.0000 chunk 636 optimal weight: 2.9990 chunk 620 optimal weight: 7.9990 chunk 469 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN K 13 ASN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN S 15 GLN S 57 ASN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 HIS 2 6 GLN ** w 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 159273 Z= 0.334 Angle : 0.686 17.092 237601 Z= 0.359 Chirality : 0.040 0.350 30136 Planarity : 0.006 0.140 13179 Dihedral : 22.837 176.980 78002 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.30 % Rotamer: Outliers : 4.76 % Allowed : 24.19 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6145 helix: 0.57 (0.11), residues: 2050 sheet: -0.39 (0.15), residues: 1212 loop : -0.76 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.007 0.001 HIS e 89 PHE 0.040 0.002 PHE w 322 TYR 0.037 0.002 TYR O 99 ARG 0.013 0.001 ARG L 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 994 time to evaluate : 6.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 8 LYS cc_start: 0.7728 (tppt) cc_final: 0.7473 (tppt) REVERT: d 154 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7360 (ptt180) REVERT: f 102 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.2399 (pmt) REVERT: i 18 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7447 (mtm110) REVERT: l 30 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8211 (mptp) REVERT: l 44 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8163 (mmtt) REVERT: l 94 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.5887 (mtp85) REVERT: n 54 ASP cc_start: 0.7600 (t0) cc_final: 0.7335 (t0) REVERT: q 7 THR cc_start: 0.7988 (m) cc_final: 0.7653 (m) REVERT: q 57 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7362 (p0) REVERT: q 77 ARG cc_start: 0.7322 (ptp90) cc_final: 0.7116 (ptt-90) REVERT: t 49 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7507 (tttp) REVERT: u 31 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5207 (mp0) REVERT: C 163 GLN cc_start: 0.8270 (tt0) cc_final: 0.7918 (tt0) REVERT: C 225 MET cc_start: 0.8823 (mtt) cc_final: 0.8407 (mtt) REVERT: C 236 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 168 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: J 31 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: J 93 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8384 (mm) REVERT: K 7 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.6970 (mmm) REVERT: K 92 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: M 66 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6804 (mmm160) REVERT: M 114 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7610 (ttt-90) REVERT: P 29 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7003 (mmmt) REVERT: R 22 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8527 (pp) REVERT: S 92 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7343 (ttm170) REVERT: V 48 MET cc_start: 0.7145 (tpt) cc_final: 0.6778 (tpt) REVERT: X 22 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8596 (mt) REVERT: X 25 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8181 (p) REVERT: 0 10 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7791 (mtt-85) outliers start: 243 outliers final: 151 residues processed: 1135 average time/residue: 2.2376 time to fit residues: 3646.5792 Evaluate side-chains 1135 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 963 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 156 LYS Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 45 GLU Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 49 LYS Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain w residue 16 SER Chi-restraints excluded: chain w residue 125 THR Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 275 VAL Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 590 GLU Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 649 VAL Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 629 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 647 optimal weight: 6.9990 chunk 693 optimal weight: 1.9990 chunk 503 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 800 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN K 13 ASN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN S 15 GLN S 57 ASN W 57 HIS 2 6 GLN w 198 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 159273 Z= 0.322 Angle : 0.685 17.104 237601 Z= 0.358 Chirality : 0.039 0.354 30136 Planarity : 0.006 0.140 13179 Dihedral : 22.819 176.969 78002 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.94 % Rotamer: Outliers : 4.68 % Allowed : 24.76 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.43 (0.10), residues: 6145 helix: 0.56 (0.11), residues: 2056 sheet: -0.40 (0.15), residues: 1189 loop : -0.76 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 97 HIS 0.007 0.001 HIS e 89 PHE 0.021 0.002 PHE r 13 TYR 0.022 0.002 TYR S 38 ARG 0.022 0.001 ARG w 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 997 time to evaluate : 6.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 113 ARG cc_start: 0.6504 (tpm170) cc_final: 0.6026 (tpm170) REVERT: d 116 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: d 128 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6592 (mtp-110) REVERT: d 154 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6927 (ptt180) REVERT: e 20 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.8075 (tmt90) REVERT: f 102 MET cc_start: 0.3612 (OUTLIER) cc_final: 0.2544 (pmt) REVERT: g 31 MET cc_start: 0.7488 (tpp) cc_final: 0.7138 (ttm) REVERT: i 18 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7476 (mtm110) REVERT: j 48 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7727 (mtt-85) REVERT: l 30 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8210 (mptp) REVERT: l 44 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8194 (mmtt) REVERT: l 94 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5861 (mtp85) REVERT: n 54 ASP cc_start: 0.7623 (t0) cc_final: 0.7401 (t0) REVERT: q 57 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7392 (p0) REVERT: t 33 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7424 (mttm) REVERT: t 49 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7510 (tttp) REVERT: u 31 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5192 (mp0) REVERT: C 163 GLN cc_start: 0.8278 (tt0) cc_final: 0.7910 (tt0) REVERT: C 225 MET cc_start: 0.8808 (mtt) cc_final: 0.8412 (mtt) REVERT: C 236 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7681 (mm-30) REVERT: D 168 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: J 31 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6644 (mm-30) REVERT: J 93 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8391 (mm) REVERT: K 92 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: M 66 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6699 (mmm160) REVERT: M 114 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7627 (ttt-90) REVERT: N 8 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8181 (mtt90) REVERT: N 64 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: P 29 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6998 (mmmt) REVERT: R 22 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8559 (pp) REVERT: R 48 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8257 (mtmm) REVERT: S 92 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: X 22 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8586 (mt) REVERT: X 25 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (p) REVERT: 0 10 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7789 (mtt-85) outliers start: 239 outliers final: 151 residues processed: 1136 average time/residue: 2.2369 time to fit residues: 3627.3190 Evaluate side-chains 1152 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 977 time to evaluate : 6.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 45 GLU Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain t residue 49 LYS Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 275 VAL Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 449 THR Chi-restraints excluded: chain w residue 590 GLU Chi-restraints excluded: chain w residue 636 SER Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 925 optimal weight: 6.9990 chunk 975 optimal weight: 0.7980 chunk 889 optimal weight: 4.9990 chunk 948 optimal weight: 0.8980 chunk 974 optimal weight: 0.9990 chunk 570 optimal weight: 10.0000 chunk 413 optimal weight: 50.0000 chunk 744 optimal weight: 0.9990 chunk 291 optimal weight: 0.3980 chunk 857 optimal weight: 5.9990 chunk 897 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 42 ASN ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN d 152 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN p 40 ASN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 150 GLN E 195 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN S 15 GLN S 57 ASN V 5 ASN W 57 HIS w 198 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 159273 Z= 0.139 Angle : 0.597 17.042 237601 Z= 0.318 Chirality : 0.033 0.383 30136 Planarity : 0.006 0.124 13179 Dihedral : 22.766 177.199 78002 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 2.88 % Allowed : 26.82 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.23 (0.10), residues: 6145 helix: 0.75 (0.11), residues: 2046 sheet: -0.28 (0.15), residues: 1175 loop : -0.68 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 201 HIS 0.007 0.001 HIS w 655 PHE 0.027 0.001 PHE w 322 TYR 0.028 0.001 TYR O 99 ARG 0.015 0.001 ARG L 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1036 time to evaluate : 6.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 128 ARG cc_start: 0.6895 (ttm-80) cc_final: 0.6483 (mtm-85) REVERT: e 20 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.8057 (tmt90) REVERT: g 31 MET cc_start: 0.7032 (tpp) cc_final: 0.6500 (ttm) REVERT: l 44 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8007 (mmtt) REVERT: n 54 ASP cc_start: 0.7526 (t0) cc_final: 0.7273 (t0) REVERT: p 35 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6229 (tmm-80) REVERT: q 57 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7264 (p0) REVERT: r 57 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7997 (ttm110) REVERT: r 61 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7822 (mtt180) REVERT: t 54 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7947 (tmm) REVERT: u 31 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5090 (mp0) REVERT: C 163 GLN cc_start: 0.8165 (tt0) cc_final: 0.7558 (tt0) REVERT: C 225 MET cc_start: 0.8801 (mtt) cc_final: 0.8439 (mtt) REVERT: C 236 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7531 (mm-30) REVERT: F 26 MET cc_start: 0.4676 (pp-130) cc_final: 0.4107 (ppp) REVERT: J 93 ILE cc_start: 0.8575 (tp) cc_final: 0.8357 (mm) REVERT: K 92 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: R 22 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8501 (pp) REVERT: R 48 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8184 (mtmm) REVERT: 0 10 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7615 (mtt-85) outliers start: 147 outliers final: 83 residues processed: 1118 average time/residue: 2.2396 time to fit residues: 3576.1797 Evaluate side-chains 1063 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 972 time to evaluate : 6.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 156 LYS Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 35 ARG Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 61 ARG Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain w residue 186 VAL Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 275 VAL Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 449 THR Chi-restraints excluded: chain w residue 623 THR Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 945 optimal weight: 5.9990 chunk 622 optimal weight: 10.0000 chunk 1002 optimal weight: 20.0000 chunk 612 optimal weight: 8.9990 chunk 475 optimal weight: 10.0000 chunk 697 optimal weight: 0.7980 chunk 1052 optimal weight: 5.9990 chunk 968 optimal weight: 9.9990 chunk 837 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 647 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN d 152 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN D 148 GLN D 150 GLN E 195 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN K 13 ASN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN S 15 GLN S 57 ASN W 57 HIS w 198 GLN ** w 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 159273 Z= 0.412 Angle : 0.744 17.299 237601 Z= 0.383 Chirality : 0.042 0.333 30136 Planarity : 0.007 0.144 13179 Dihedral : 22.758 176.618 78000 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 2.88 % Allowed : 27.70 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 6145 helix: 0.55 (0.11), residues: 2053 sheet: -0.47 (0.15), residues: 1207 loop : -0.74 (0.11), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 248 HIS 0.009 0.002 HIS i 81 PHE 0.046 0.002 PHE i 20 TYR 0.050 0.002 TYR O 99 ARG 0.020 0.001 ARG k 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12290 Ramachandran restraints generated. 6145 Oldfield, 0 Emsley, 6145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 985 time to evaluate : 6.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 128 ARG cc_start: 0.6948 (ttm-80) cc_final: 0.6607 (mtm-85) REVERT: d 145 ILE cc_start: 0.7928 (mp) cc_final: 0.7578 (mm) REVERT: g 31 MET cc_start: 0.7537 (tpp) cc_final: 0.7054 (ttm) REVERT: j 48 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: l 10 LYS cc_start: 0.7638 (tptt) cc_final: 0.7305 (pttt) REVERT: l 44 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8132 (mmtt) REVERT: l 94 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.5883 (mtp85) REVERT: n 54 ASP cc_start: 0.7747 (t0) cc_final: 0.7509 (t0) REVERT: p 35 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6339 (tmm160) REVERT: q 57 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7446 (p0) REVERT: r 61 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: u 31 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5184 (mp0) REVERT: C 163 GLN cc_start: 0.8315 (tt0) cc_final: 0.7943 (tt0) REVERT: C 225 MET cc_start: 0.8853 (mtt) cc_final: 0.8464 (mtt) REVERT: C 236 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 168 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: J 34 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7490 (ttm110) REVERT: J 93 ILE cc_start: 0.8653 (tp) cc_final: 0.8405 (mm) REVERT: K 92 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: O 111 ARG cc_start: 0.5990 (mpt90) cc_final: 0.5729 (mmt-90) REVERT: R 22 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8560 (pp) REVERT: R 48 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8249 (mtmm) REVERT: 0 10 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7800 (mtt-85) REVERT: 1 27 LYS cc_start: 0.8359 (mttt) cc_final: 0.8077 (mttp) REVERT: w 101 ARG cc_start: 0.5999 (mmt180) cc_final: 0.5709 (mmt180) REVERT: w 641 MET cc_start: 0.6851 (ppp) cc_final: 0.6430 (pmm) outliers start: 147 outliers final: 98 residues processed: 1066 average time/residue: 2.2366 time to fit residues: 3410.8771 Evaluate side-chains 1078 residues out of total 5106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 971 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 156 LYS Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 11 HIS Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 CYS Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 35 ARG Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 53 CYS Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 61 ARG Chi-restraints excluded: chain r residue 68 LEU Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain u residue 31 GLU Chi-restraints excluded: chain u residue 43 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain 5 residue 45 THR Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 10 ARG Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain w residue 220 GLN Chi-restraints excluded: chain w residue 228 GLU Chi-restraints excluded: chain w residue 265 THR Chi-restraints excluded: chain w residue 275 VAL Chi-restraints excluded: chain w residue 343 VAL Chi-restraints excluded: chain w residue 441 GLU Chi-restraints excluded: chain w residue 449 THR Chi-restraints excluded: chain w residue 455 GLN Chi-restraints excluded: chain w residue 623 THR Chi-restraints excluded: chain w residue 658 VAL Chi-restraints excluded: chain w residue 681 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 513 optimal weight: 10.0000 chunk 665 optimal weight: 10.0000 chunk 892 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 772 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 839 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 861 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN d 152 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN k 24 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN r 54 GLN ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN J 67 ASN K 13 ASN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN S 15 GLN W 57 HIS ** w 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 454 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149992 restraints weight = 212908.551| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.24 r_work: 0.3391 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 159273 Z= 0.259 Angle : 0.659 17.085 237601 Z= 0.347 Chirality : 0.037 0.356 30136 Planarity : 0.006 0.135 13179 Dihedral : 22.762 177.216 78000 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.25 % Rotamer: Outliers : 2.74 % Allowed : 28.03 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.41 (0.10), residues: 6145 helix: 0.61 (0.11), residues: 2048 sheet: -0.46 (0.15), residues: 1181 loop : -0.74 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.008 0.001 HIS i 81 PHE 0.038 0.002 PHE w 322 TYR 0.031 0.002 TYR S 38 ARG 0.017 0.001 ARG k 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49458.57 seconds wall clock time: 858 minutes 44.07 seconds (51524.07 seconds total)