Starting phenix.real_space_refine on Sun Nov 19 03:44:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eth_24409/11_2023/8eth_24409.pdb" } resolution = 3.8 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1508 5.49 5 S 116 5.16 5 C 43000 2.51 5 N 14348 2.21 5 O 18604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 GLU 52": "OE1" <-> "OE2" Residue "5 TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 166": "OD1" <-> "OD2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ASP 135": "OD1" <-> "OD2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 114": "OD1" <-> "OD2" Residue "O TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 7": "OE1" <-> "OE2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "i GLU 44": "OE1" <-> "OE2" Residue "m TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 55": "OE1" <-> "OE2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "t TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 77577 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 27887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1303, 27887 Classifications: {'RNA': 1303} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 84, 'rna3p_pur': 591, 'rna3p_pyr': 491} Link IDs: {'rna2p': 221, 'rna3p': 1081} Chain breaks: 31 Chain: "2" Number of atoms: 2764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2764 Classifications: {'RNA': 130} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 8, 'rna3p_pur': 52, 'rna3p_pyr': 55} Link IDs: {'rna2p': 23, 'rna3p': 106} Chain breaks: 3 Chain: "3" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1572 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 183} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "4" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1756 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 200} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2640 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 16, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 30, 'rna3p': 44} Chain breaks: 3 Chain: "A" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1981 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1557 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 303} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1016 Unresolved non-hydrogen angles: 1283 Unresolved non-hydrogen dihedrals: 862 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 526 Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2564 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3095 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 18, 'TRANS': 403} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1328 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1939 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain: "G" Number of atoms: 1277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 bond proxies already assigned to first conformer: 1261 Chain: "H" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 542 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 86} Chain breaks: 3 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "J" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 414 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "K" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1845 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 232} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "M" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1464 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1034 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 2 Chain: "Q" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1033 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 129} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1172 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 95 Chain: "V" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 210 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 282 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 111 Chain: "e" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 960 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "i" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 767 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "j" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 559 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "m" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1029 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 198} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 19, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 443 Chain: "o" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1043 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 130} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "r" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 254 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 119 Chain: "t" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1228 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 164 Chain: "u" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 287 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Chain: "v" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "x" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2497 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 292} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "y" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 842 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 270 Chain: "T" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 15} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 67879 SG CYS j 19 87.187 92.993 165.328 1.00 5.82 S ATOM 67907 SG CYS j 22 89.463 93.472 162.258 1.00 4.10 S ATOM 68003 SG CYS j 34 88.125 90.147 162.885 1.00 6.74 S ATOM 68020 SG CYS j 37 90.657 91.577 165.361 1.00 4.26 S Time building chain proxies: 31.27, per 1000 atoms: 0.40 Number of scatterers: 77577 At special positions: 0 Unit cell: (223.66, 196.1, 311.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 1508 15.00 O 18604 8.00 N 14348 7.00 C 43000 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: 32.16 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11686 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 55 sheets defined 42.8% alpha, 12.1% beta 471 base pairs and 864 stacking pairs defined. Time for finding SS restraints: 26.50 Creating SS restraints... Processing helix chain '3' and resid 5 through 13 removed outlier: 3.523A pdb=" N HIS 3 13 " --> pdb=" O GLN 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 70 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 128 Processing helix chain '3' and resid 137 through 156 removed outlier: 3.668A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 171 Processing helix chain '3' and resid 182 through 191 removed outlier: 4.077A pdb=" N LYS 3 188 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL 3 189 " --> pdb=" O ILE 3 185 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 3 190 " --> pdb=" O TRP 3 186 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 12 removed outlier: 3.769A pdb=" N ALA 4 12 " --> pdb=" O ILE 4 8 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 12' Processing helix chain '4' and resid 15 through 31 removed outlier: 3.570A pdb=" N GLN 4 27 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 54 Processing helix chain '4' and resid 57 through 70 removed outlier: 3.753A pdb=" N SER 4 65 " --> pdb=" O GLN 4 61 " (cutoff:3.500A) Processing helix chain '4' and resid 76 through 78 No H-bonds generated for 'chain '4' and resid 76 through 78' Processing helix chain '4' and resid 79 through 95 removed outlier: 3.507A pdb=" N ARG 4 93 " --> pdb=" O GLU 4 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU 4 94 " --> pdb=" O THR 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 102 through 128 removed outlier: 3.687A pdb=" N PHE 4 106 " --> pdb=" O ARG 4 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS 4 126 " --> pdb=" O GLN 4 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR 4 127 " --> pdb=" O THR 4 123 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 143 removed outlier: 3.519A pdb=" N VAL 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 154 through 173 removed outlier: 3.874A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR 4 166 " --> pdb=" O ALA 4 162 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU 4 167 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 193 Processing helix chain '4' and resid 195 through 206 Proline residue: 4 203 - end of helix Processing helix chain '4' and resid 209 through 213 removed outlier: 3.991A pdb=" N TYR 4 212 " --> pdb=" O VAL 4 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR 4 213 " --> pdb=" O SER 4 210 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 209 through 213' Processing helix chain '5' and resid 40 through 44 Processing helix chain '5' and resid 83 through 88 removed outlier: 3.858A pdb=" N GLU 5 88 " --> pdb=" O SER 5 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 250 through 264 removed outlier: 4.088A pdb=" N ILE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 removed outlier: 3.542A pdb=" N ARG A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 140 through 155 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.650A pdb=" N GLY C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.935A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.182A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.702A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.582A pdb=" N ASP D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.647A pdb=" N LEU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.575A pdb=" N GLY D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.593A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 290 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 416 through 425 removed outlier: 4.015A pdb=" N HIS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 425 " --> pdb=" O ILE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 455 removed outlier: 3.992A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 483 through 503 removed outlier: 3.605A pdb=" N GLN D 487 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'E' and resid 120 through 125 removed outlier: 3.501A pdb=" N PHE E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix removed outlier: 3.959A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 16 through 80 removed outlier: 3.579A pdb=" N ALA F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.812A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 240 through 247 removed outlier: 4.354A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.568A pdb=" N GLN G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 144 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.970A pdb=" N LEU G 186 " --> pdb=" O AASN G 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'H' and resid 21 through 25 Processing helix chain 'H' and resid 61 through 85 removed outlier: 3.596A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 161 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 160 Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 42 through 46 removed outlier: 4.020A pdb=" N GLU K 46 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 105 removed outlier: 4.116A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.630A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.647A pdb=" N PHE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 removed outlier: 3.800A pdb=" N LEU K 154 " --> pdb=" O LEU K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'K' and resid 174 through 188 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 231 through 234 removed outlier: 3.652A pdb=" N LYS K 234 " --> pdb=" O ASP K 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 231 through 234' Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 4.357A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE L 93 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.566A pdb=" N LEU L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 103 removed outlier: 3.569A pdb=" N LYS M 94 " --> pdb=" O SER M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 removed outlier: 3.734A pdb=" N GLU M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.860A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 32 Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 152 Processing helix chain 'N' and resid 153 through 157 Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 190 through 194 removed outlier: 3.732A pdb=" N THR N 194 " --> pdb=" O LEU N 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 190 through 194' Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 60 removed outlier: 3.670A pdb=" N ASN O 51 " --> pdb=" O HIS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 removed outlier: 3.656A pdb=" N MET O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 121 through 125 Processing helix chain 'O' and resid 139 through 147 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.754A pdb=" N LYS O 178 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 Processing helix chain 'O' and resid 193 through 196 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 84 through 105 Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.720A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.782A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'S' and resid 32 through 46 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 110 through 116 removed outlier: 3.872A pdb=" N SER V 114 " --> pdb=" O GLU V 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE V 116 " --> pdb=" O LYS V 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.990A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 42 Processing helix chain 'Y' and resid 74 through 76 No H-bonds generated for 'chain 'Y' and resid 74 through 76' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'b' and resid 16 through 27 Processing helix chain 'b' and resid 43 through 62 Processing helix chain 'b' and resid 124 through 138 Processing helix chain 'b' and resid 156 through 160 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 80 removed outlier: 3.827A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 86 removed outlier: 4.341A pdb=" N MET e 84 " --> pdb=" O LEU e 81 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 112 removed outlier: 3.610A pdb=" N ALA e 111 " --> pdb=" O GLU e 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.582A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 Processing helix chain 'h' and resid 12 through 35 removed outlier: 3.560A pdb=" N GLN h 25 " --> pdb=" O GLN h 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU h 26 " --> pdb=" O GLU h 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN h 33 " --> pdb=" O SER h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 72 Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 removed outlier: 3.536A pdb=" N LYS i 28 " --> pdb=" O SER i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.782A pdb=" N GLY i 47 " --> pdb=" O ARG i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 61 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 99 Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 64 through 75 removed outlier: 4.077A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'm' and resid 221 through 226 removed outlier: 3.691A pdb=" N ARG m 224 " --> pdb=" O PRO m 221 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 removed outlier: 3.646A pdb=" N ALA m 241 " --> pdb=" O GLN m 237 " (cutoff:3.500A) Processing helix chain 'm' and resid 249 through 258 removed outlier: 3.711A pdb=" N ARG m 258 " --> pdb=" O ALA m 254 " (cutoff:3.500A) Processing helix chain 'n' and resid 117 through 123 Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 133 through 145 removed outlier: 3.875A pdb=" N THR n 145 " --> pdb=" O PHE n 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 217 through 242 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 366 through 377 Processing helix chain 'n' and resid 420 through 429 Processing helix chain 'o' and resid 117 through 129 removed outlier: 3.819A pdb=" N GLN o 127 " --> pdb=" O MET o 123 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 166 Processing helix chain 'o' and resid 187 through 192 removed outlier: 4.292A pdb=" N PHE o 191 " --> pdb=" O GLU o 188 " (cutoff:3.500A) Processing helix chain 'o' and resid 202 through 213 Processing helix chain 'o' and resid 216 through 238 removed outlier: 3.747A pdb=" N LYS o 234 " --> pdb=" O LYS o 230 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG o 236 " --> pdb=" O LYS o 232 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 13 Processing helix chain 'r' and resid 20 through 42 removed outlier: 4.147A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 57 removed outlier: 3.515A pdb=" N LYS r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 76 removed outlier: 3.784A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 112 removed outlier: 3.523A pdb=" N ARG t 106 " --> pdb=" O PRO t 102 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS t 107 " --> pdb=" O PRO t 103 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL t 108 " --> pdb=" O LYS t 104 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG t 110 " --> pdb=" O ARG t 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU t 112 " --> pdb=" O VAL t 108 " (cutoff:3.500A) Processing helix chain 't' and resid 126 through 137 removed outlier: 3.929A pdb=" N ALA t 130 " --> pdb=" O ASN t 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN t 131 " --> pdb=" O LYS t 127 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET t 132 " --> pdb=" O ALA t 128 " (cutoff:3.500A) Processing helix chain 't' and resid 146 through 156 Processing helix chain 't' and resid 171 through 179 removed outlier: 3.727A pdb=" N ILE t 175 " --> pdb=" O ASP t 171 " (cutoff:3.500A) Processing helix chain 't' and resid 186 through 195 Processing helix chain 't' and resid 200 through 208 Processing helix chain 't' and resid 239 through 249 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 58 removed outlier: 3.899A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 removed outlier: 3.668A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 36 through 40 removed outlier: 3.635A pdb=" N TRP v 40 " --> pdb=" O GLN v 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.675A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 194 through 207 removed outlier: 3.921A pdb=" N LYS v 206 " --> pdb=" O TYR v 202 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA v 207 " --> pdb=" O ILE v 203 " (cutoff:3.500A) Processing helix chain 'x' and resid 6 through 39 Processing helix chain 'x' and resid 39 through 48 removed outlier: 3.796A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU x 45 " --> pdb=" O GLU x 41 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 78 Processing helix chain 'x' and resid 83 through 88 removed outlier: 3.591A pdb=" N PHE x 87 " --> pdb=" O PHE x 83 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 119 removed outlier: 4.128A pdb=" N GLU x 114 " --> pdb=" O ASP x 110 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 143 removed outlier: 3.856A pdb=" N GLU x 138 " --> pdb=" O HIS x 134 " (cutoff:3.500A) Processing helix chain 'x' and resid 205 through 217 Processing helix chain 'x' and resid 224 through 227 Processing helix chain 'x' and resid 294 through 298 Processing helix chain 'y' and resid 12 through 17 Processing helix chain 'y' and resid 33 through 41 Processing helix chain 'y' and resid 41 through 46 removed outlier: 4.186A pdb=" N VAL y 45 " --> pdb=" O GLU y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 52 through 56 Processing helix chain 'y' and resid 66 through 70 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 100 through 102 No H-bonds generated for 'chain 'y' and resid 100 through 102' Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 132 Processing helix chain 'y' and resid 141 through 145 removed outlier: 3.501A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.506A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) Processing helix chain 'y' and resid 193 through 196 No H-bonds generated for 'chain 'y' and resid 193 through 196' Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 56 Processing sheet with id=AA3, first strand: chain '3' and resid 133 through 135 Processing sheet with id=AA4, first strand: chain '5' and resid 33 through 37 removed outlier: 4.554A pdb=" N GLN 5 11 " --> pdb=" O ASP 5 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS 5 2 " --> pdb=" O ILE 5 342 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER 5 338 " --> pdb=" O GLY 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 50 through 51 removed outlier: 6.592A pdb=" N CYS 5 66 " --> pdb=" O SER 5 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN 5 68 " --> pdb=" O ILE 5 75 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE 5 75 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain '5' and resid 132 through 135 removed outlier: 5.275A pdb=" N GLY 5 147 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP 5 151 " --> pdb=" O GLY 5 147 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL 5 152 " --> pdb=" O GLN 5 181 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN 5 181 " --> pdb=" O VAL 5 152 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU 5 154 " --> pdb=" O VAL 5 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 198 through 203 removed outlier: 3.755A pdb=" N PHE 5 225 " --> pdb=" O TYR 5 237 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER 5 247 " --> pdb=" O PHE 5 236 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP 5 238 " --> pdb=" O PRO 5 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 256 through 262 removed outlier: 6.712A pdb=" N ALA 5 271 " --> pdb=" O SER 5 257 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL 5 259 " --> pdb=" O TYR 5 269 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR 5 269 " --> pdb=" O VAL 5 259 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU 5 261 " --> pdb=" O LEU 5 267 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU 5 267 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN 5 276 " --> pdb=" O ASP 5 272 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE 5 277 " --> pdb=" O ARG 5 290 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARG 5 290 " --> pdb=" O ILE 5 277 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE 5 279 " --> pdb=" O ILE 5 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 298 through 304 removed outlier: 3.648A pdb=" N VAL 5 307 " --> pdb=" O LEU 5 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY 5 312 " --> pdb=" O ASN 5 316 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP 5 321 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.912A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 73 current: chain 'A' and resid 108 through 115 removed outlier: 3.876A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 126 current: chain 'A' and resid 188 through 194 removed outlier: 3.936A pdb=" N PHE A 200 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 243 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU A 234 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL A 241 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 59 removed outlier: 4.001A pdb=" N GLU B 74 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AB6, first strand: chain 'B' and resid 89 through 95 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 98 through 100 current: chain 'B' and resid 179 through 182 Processing sheet with id=AB7, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AB8, first strand: chain 'B' and resid 218 through 220 Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 23 removed outlier: 4.987A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC2, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.428A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.418A pdb=" N VAL D 339 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N CYS D 392 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL D 341 " --> pdb=" O CYS D 392 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE D 408 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE D 440 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN D 410 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 314 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR D 315 " --> pdb=" O PHE D 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.705A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.571A pdb=" N TYR F 82 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 84 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 212 through 213 removed outlier: 3.938A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC9, first strand: chain 'K' and resid 198 through 205 removed outlier: 6.444A pdb=" N VAL K 53 " --> pdb=" O CYS K 203 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA K 237 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASN K 253 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE K 239 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.875A pdb=" N SER K 193 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.884A pdb=" N ALA K 87 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE K 115 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU K 89 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE K 140 " --> pdb=" O VAL K 166 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL K 168 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA K 142 " --> pdb=" O VAL K 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.132A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD5, first strand: chain 'M' and resid 8 through 9 Processing sheet with id=AD6, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.815A pdb=" N GLN M 49 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.679A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.011A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL O 34 " --> pdb=" O GLN O 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE1, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.660A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU P 147 " --> pdb=" O VAL P 117 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE P 149 " --> pdb=" O LYS P 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE3, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.753A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR Q 81 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.163A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 87 through 95 removed outlier: 4.209A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AE7, first strand: chain 'Y' and resid 98 through 99 removed outlier: 3.680A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 85 through 87 Processing sheet with id=AE9, first strand: chain 'e' and resid 69 through 73 removed outlier: 5.830A pdb=" N LYS e 69 " --> pdb=" O ALA e 90 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU e 92 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE e 71 " --> pdb=" O GLU e 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'f' and resid 65 through 68 removed outlier: 4.950A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF3, first strand: chain 'n' and resid 177 through 182 removed outlier: 6.640A pdb=" N GLN n 190 " --> pdb=" O ARG n 178 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA n 180 " --> pdb=" O TYR n 188 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR n 188 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'n' and resid 358 through 360 removed outlier: 6.944A pdb=" N PHE n 359 " --> pdb=" O ILE n 403 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'o' and resid 131 through 138 removed outlier: 4.202A pdb=" N ARG o 133 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU o 152 " --> pdb=" O ARG o 133 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR o 148 " --> pdb=" O SER o 137 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR o 169 " --> pdb=" O LEU o 176 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 't' and resid 211 through 212 removed outlier: 5.004A pdb=" N ASN t 119 " --> pdb=" O ARG t 94 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG t 94 " --> pdb=" O ASN t 119 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL t 92 " --> pdb=" O VAL t 121 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY t 143 " --> pdb=" O PHE t 91 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS t 237 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR t 142 " --> pdb=" O CYS t 237 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 't' and resid 161 through 162 Processing sheet with id=AF8, first strand: chain 'u' and resid 20 through 21 Processing sheet with id=AF9, first strand: chain 'x' and resid 96 through 100 removed outlier: 6.636A pdb=" N LEU x 96 " --> pdb=" O GLU x 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 123 through 124 current: chain 'x' and resid 158 through 165 WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 171 through 174 current: chain 'x' and resid 229 through 236 WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 259 through 265 current: chain 'x' and resid 289 through 292 Processing sheet with id=AG1, first strand: chain 'y' and resid 197 through 198 1970 hydrogen bonds defined for protein. 5607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1134 hydrogen bonds 1836 hydrogen bond angles 0 basepair planarities 471 basepair parallelities 864 stacking parallelities Total time for adding SS restraints: 49.66 Time building geometry restraints manager: 34.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10216 1.32 - 1.44: 29879 1.44 - 1.57: 38817 1.57 - 1.69: 2976 1.69 - 1.82: 187 Bond restraints: 82075 Sorted by residual: bond pdb=" C VAL 3 11 " pdb=" O VAL 3 11 " ideal model delta sigma weight residual 1.233 1.194 0.039 1.22e-02 6.72e+03 1.01e+01 bond pdb=" CB VAL C 315 " pdb=" CG1 VAL C 315 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.43e+00 bond pdb=" C PHE x 119 " pdb=" O PHE x 119 " ideal model delta sigma weight residual 1.249 1.230 0.019 8.50e-03 1.38e+04 5.07e+00 bond pdb=" CA GLN h 84 " pdb=" C GLN h 84 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.30e-02 5.92e+03 4.70e+00 bond pdb=" C LEU Q 35 " pdb=" O LEU Q 35 " ideal model delta sigma weight residual 1.237 1.212 0.024 1.17e-02 7.31e+03 4.36e+00 ... (remaining 82070 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.55: 7977 105.55 - 112.75: 46430 112.75 - 119.95: 28405 119.95 - 127.15: 31775 127.15 - 134.35: 3686 Bond angle restraints: 118273 Sorted by residual: angle pdb=" C ALA L 47 " pdb=" N PRO L 48 " pdb=" CA PRO L 48 " ideal model delta sigma weight residual 120.04 113.05 6.99 1.08e+00 8.57e-01 4.19e+01 angle pdb=" C PHE H 86 " pdb=" CA PHE H 86 " pdb=" CB PHE H 86 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 angle pdb=" N ALA L 47 " pdb=" CA ALA L 47 " pdb=" C ALA L 47 " ideal model delta sigma weight residual 109.81 119.55 -9.74 2.21e+00 2.05e-01 1.94e+01 angle pdb=" C HIS K 227 " pdb=" N ILE K 228 " pdb=" CA ILE K 228 " ideal model delta sigma weight residual 123.16 119.03 4.13 1.06e+00 8.90e-01 1.51e+01 angle pdb=" O3' U 6 8 " pdb=" C3' U 6 8 " pdb=" C2' U 6 8 " ideal model delta sigma weight residual 109.50 115.14 -5.64 1.50e+00 4.44e-01 1.41e+01 ... (remaining 118268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 44444 35.72 - 71.43: 1592 71.43 - 107.15: 139 107.15 - 142.87: 15 142.87 - 178.58: 29 Dihedral angle restraints: 46219 sinusoidal: 28286 harmonic: 17933 Sorted by residual: dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual 200.00 21.42 178.58 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 300 " pdb=" C1' U 1 300 " pdb=" N1 U 1 300 " pdb=" C2 U 1 300 " ideal model delta sinusoidal sigma weight residual -160.00 18.44 -178.44 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual -160.00 14.75 -174.75 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 46216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 12932 0.060 - 0.120: 1562 0.120 - 0.181: 153 0.181 - 0.241: 21 0.241 - 0.301: 3 Chirality restraints: 14671 Sorted by residual: chirality pdb=" C3' U 6 8 " pdb=" C4' U 6 8 " pdb=" O3' U 6 8 " pdb=" C2' U 6 8 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1' C 1 723 " pdb=" O4' C 1 723 " pdb=" C2' C 1 723 " pdb=" N1 C 1 723 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' A 13431 " pdb=" C3' A 13431 " pdb=" O2' A 13431 " pdb=" C1' A 13431 " both_signs ideal model delta sigma weight residual False -2.75 -2.48 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 14668 not shown) Planarity restraints: 9581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 109 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO O 110 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO O 110 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO O 110 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP x 39 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO x 40 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO x 40 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO x 40 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 349 " 0.043 2.00e-02 2.50e+03 1.83e-02 1.00e+01 pdb=" N9 G 1 349 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G 1 349 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G 1 349 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 349 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 349 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G 1 349 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G 1 349 " 0.009 2.00e-02 2.50e+03 pdb=" C2 G 1 349 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 1 349 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G 1 349 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G 1 349 " -0.011 2.00e-02 2.50e+03 ... (remaining 9578 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 2392 2.65 - 3.21: 69142 3.21 - 3.78: 144403 3.78 - 4.34: 197482 4.34 - 4.90: 277942 Nonbonded interactions: 691361 Sorted by model distance: nonbonded pdb=" O2' A 1 816 " pdb=" OP2 G 1 817 " model vdw 2.088 2.440 nonbonded pdb=" O2' A 6 106 " pdb=" O4' A 6 107 " model vdw 2.127 2.440 nonbonded pdb=" O LEU t 109 " pdb=" N LEU t 114 " model vdw 2.196 2.520 nonbonded pdb=" OP2 A 13369 " pdb=" NH2 ARG E 64 " model vdw 2.200 2.520 nonbonded pdb=" O LYS N 157 " pdb=" NH2 ARG N 162 " model vdw 2.202 2.520 ... (remaining 691356 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 28.150 Check model and map are aligned: 0.850 Set scattering table: 0.570 Process input model: 219.030 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 82075 Z= 0.348 Angle : 0.616 9.739 118273 Z= 0.321 Chirality : 0.040 0.301 14671 Planarity : 0.006 0.098 9581 Dihedral : 16.487 178.584 34533 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.22 % Favored : 94.56 % Rotamer: Outliers : 0.53 % Allowed : 18.70 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6021 helix: 0.63 (0.11), residues: 2319 sheet: -0.35 (0.20), residues: 728 loop : -1.04 (0.11), residues: 2974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 573 time to evaluate : 5.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 580 average time/residue: 0.7783 time to fit residues: 757.0120 Evaluate side-chains 566 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 555 time to evaluate : 5.023 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5475 time to fit residues: 17.5950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 631 optimal weight: 30.0000 chunk 566 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 382 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 586 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 356 optimal weight: 0.6980 chunk 436 optimal weight: 1.9990 chunk 679 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN C 159 GLN ** K 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 82075 Z= 0.257 Angle : 0.601 9.130 118273 Z= 0.309 Chirality : 0.039 0.257 14671 Planarity : 0.005 0.074 9581 Dihedral : 15.009 178.523 24652 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 2.23 % Allowed : 18.46 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 6021 helix: 1.03 (0.11), residues: 2389 sheet: -0.41 (0.20), residues: 753 loop : -0.98 (0.12), residues: 2879 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 578 time to evaluate : 4.978 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 outliers start: 90 outliers final: 45 residues processed: 642 average time/residue: 0.8420 time to fit residues: 921.6728 Evaluate side-chains 603 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 558 time to evaluate : 5.005 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 45 outliers final: 1 residues processed: 45 average time/residue: 0.6126 time to fit residues: 58.2968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 377 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 565 optimal weight: 5.9990 chunk 462 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 680 optimal weight: 0.0040 chunk 735 optimal weight: 20.0000 chunk 606 optimal weight: 5.9990 chunk 674 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 545 optimal weight: 0.0770 overall best weight: 1.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 68 ASN 5 71 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN D 227 GLN D 488 GLN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 ASN ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 125 ASN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 82075 Z= 0.209 Angle : 0.554 8.209 118273 Z= 0.287 Chirality : 0.038 0.239 14671 Planarity : 0.004 0.070 9581 Dihedral : 14.911 179.883 24652 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.92 % Favored : 94.86 % Rotamer: Outliers : 2.27 % Allowed : 19.09 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 6021 helix: 1.28 (0.11), residues: 2396 sheet: -0.39 (0.20), residues: 752 loop : -0.89 (0.12), residues: 2873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 597 time to evaluate : 5.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 44 residues processed: 665 average time/residue: 0.7720 time to fit residues: 867.4727 Evaluate side-chains 605 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 561 time to evaluate : 4.961 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5525 time to fit residues: 52.6798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 672 optimal weight: 40.0000 chunk 511 optimal weight: 0.7980 chunk 353 optimal weight: 0.0050 chunk 75 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 456 optimal weight: 2.9990 chunk 682 optimal weight: 30.0000 chunk 723 optimal weight: 2.9990 chunk 356 optimal weight: 0.6980 chunk 647 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 34 GLN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN D 227 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 82075 Z= 0.244 Angle : 0.573 10.978 118273 Z= 0.295 Chirality : 0.039 0.245 14671 Planarity : 0.005 0.061 9581 Dihedral : 14.885 179.617 24652 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.67 % Favored : 95.11 % Rotamer: Outliers : 2.01 % Allowed : 20.05 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6021 helix: 1.36 (0.11), residues: 2405 sheet: -0.39 (0.20), residues: 756 loop : -0.86 (0.12), residues: 2860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 587 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 42 residues processed: 642 average time/residue: 0.8125 time to fit residues: 884.7334 Evaluate side-chains 610 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 568 time to evaluate : 5.129 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.6838 time to fit residues: 59.1673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 602 optimal weight: 1.9990 chunk 410 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 chunk 538 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 616 optimal weight: 20.0000 chunk 499 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 648 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 82075 Z= 0.433 Angle : 0.694 10.787 118273 Z= 0.351 Chirality : 0.044 0.313 14671 Planarity : 0.006 0.092 9581 Dihedral : 15.114 178.076 24652 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.07 % Favored : 94.70 % Rotamer: Outliers : 1.89 % Allowed : 21.02 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6021 helix: 1.15 (0.11), residues: 2413 sheet: -0.54 (0.19), residues: 760 loop : -0.97 (0.12), residues: 2848 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 575 time to evaluate : 5.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 42 residues processed: 630 average time/residue: 0.7964 time to fit residues: 845.7057 Evaluate side-chains 598 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 556 time to evaluate : 5.047 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.5629 time to fit residues: 51.5359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 243 optimal weight: 1.9990 chunk 651 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 723 optimal weight: 0.9980 chunk 600 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 379 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 117 GLN 5 71 GLN A 59 HIS ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 69 GLN H 65 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 82075 Z= 0.207 Angle : 0.558 11.099 118273 Z= 0.288 Chirality : 0.038 0.247 14671 Planarity : 0.004 0.071 9581 Dihedral : 14.927 179.925 24652 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.43 % Rotamer: Outliers : 1.33 % Allowed : 21.92 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 6021 helix: 1.35 (0.11), residues: 2409 sheet: -0.55 (0.19), residues: 761 loop : -0.86 (0.12), residues: 2851 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 584 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 19 residues processed: 617 average time/residue: 0.8161 time to fit residues: 844.8137 Evaluate side-chains 585 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 566 time to evaluate : 5.052 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6311 time to fit residues: 28.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 697 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 412 optimal weight: 10.0000 chunk 528 optimal weight: 3.9990 chunk 409 optimal weight: 0.2980 chunk 609 optimal weight: 7.9990 chunk 404 optimal weight: 0.6980 chunk 720 optimal weight: 0.9990 chunk 451 optimal weight: 0.0000 chunk 439 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN C 316 GLN D 227 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 237 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 82075 Z= 0.135 Angle : 0.516 10.575 118273 Z= 0.267 Chirality : 0.036 0.249 14671 Planarity : 0.004 0.060 9581 Dihedral : 14.725 179.689 24652 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 0.80 % Allowed : 22.33 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 6021 helix: 1.55 (0.11), residues: 2416 sheet: -0.44 (0.20), residues: 755 loop : -0.75 (0.12), residues: 2850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 600 time to evaluate : 4.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 617 average time/residue: 0.7971 time to fit residues: 830.2750 Evaluate side-chains 581 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 569 time to evaluate : 5.212 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5947 time to fit residues: 19.9905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 446 optimal weight: 6.9990 chunk 287 optimal weight: 0.7980 chunk 430 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 458 optimal weight: 4.9990 chunk 491 optimal weight: 0.9980 chunk 356 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 566 optimal weight: 40.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN P 54 HIS m 237 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 82075 Z= 0.400 Angle : 0.669 10.107 118273 Z= 0.338 Chirality : 0.043 0.300 14671 Planarity : 0.006 0.083 9581 Dihedral : 14.929 178.817 24652 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 0.97 % Allowed : 22.79 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 6021 helix: 1.36 (0.11), residues: 2401 sheet: -0.57 (0.20), residues: 756 loop : -0.88 (0.12), residues: 2864 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 571 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 590 average time/residue: 0.8260 time to fit residues: 814.9654 Evaluate side-chains 583 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 557 time to evaluate : 5.014 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5865 time to fit residues: 35.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 655 optimal weight: 10.0000 chunk 690 optimal weight: 1.9990 chunk 630 optimal weight: 9.9990 chunk 671 optimal weight: 30.0000 chunk 404 optimal weight: 0.9990 chunk 292 optimal weight: 0.5980 chunk 527 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 607 optimal weight: 4.9990 chunk 635 optimal weight: 6.9990 chunk 669 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 117 GLN ** 5 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN m 237 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 82075 Z= 0.201 Angle : 0.556 10.504 118273 Z= 0.286 Chirality : 0.037 0.248 14671 Planarity : 0.004 0.061 9581 Dihedral : 14.786 179.767 24652 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.41 % Favored : 95.39 % Rotamer: Outliers : 0.63 % Allowed : 22.96 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 6021 helix: 1.48 (0.11), residues: 2405 sheet: -0.48 (0.20), residues: 748 loop : -0.82 (0.12), residues: 2868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 570 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 581 average time/residue: 0.8204 time to fit residues: 794.4254 Evaluate side-chains 575 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 562 time to evaluate : 4.990 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6655 time to fit residues: 21.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 441 optimal weight: 7.9990 chunk 710 optimal weight: 0.9990 chunk 433 optimal weight: 5.9990 chunk 337 optimal weight: 0.8980 chunk 493 optimal weight: 0.6980 chunk 745 optimal weight: 20.0000 chunk 685 optimal weight: 4.9990 chunk 593 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 458 optimal weight: 2.9990 chunk 363 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 51 HIS ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 82075 Z= 0.203 Angle : 0.554 12.681 118273 Z= 0.285 Chirality : 0.037 0.245 14671 Planarity : 0.004 0.062 9581 Dihedral : 14.689 179.958 24652 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.34 % Rotamer: Outliers : 0.29 % Allowed : 23.56 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 6021 helix: 1.52 (0.11), residues: 2411 sheet: -0.44 (0.20), residues: 748 loop : -0.78 (0.12), residues: 2862 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 571 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 574 average time/residue: 0.8209 time to fit residues: 790.3921 Evaluate side-chains 568 residues out of total 5338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 563 time to evaluate : 4.971 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6500 time to fit residues: 11.9575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 471 optimal weight: 0.9990 chunk 632 optimal weight: 50.0000 chunk 181 optimal weight: 0.9980 chunk 547 optimal weight: 50.0000 chunk 87 optimal weight: 10.0000 chunk 164 optimal weight: 0.1980 chunk 594 optimal weight: 0.8980 chunk 248 optimal weight: 50.0000 chunk 610 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 34 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 316 ASN C 159 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS m 237 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105005 restraints weight = 187758.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105146 restraints weight = 446276.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104843 restraints weight = 317677.530| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 82075 Z= 0.258 Angle : 0.584 11.905 118273 Z= 0.299 Chirality : 0.039 0.250 14671 Planarity : 0.005 0.063 9581 Dihedral : 14.705 179.755 24652 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.54 % Favored : 95.26 % Rotamer: Outliers : 0.53 % Allowed : 23.56 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 6021 helix: 1.48 (0.11), residues: 2404 sheet: -0.48 (0.20), residues: 750 loop : -0.80 (0.12), residues: 2867 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14201.92 seconds wall clock time: 253 minutes 47.16 seconds (15227.16 seconds total)