Starting phenix.real_space_refine (version: dev) on Sat Dec 17 14:32:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etg_24397/12_2022/8etg_24397.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "3 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O ASP 152": "OD1" <-> "OD2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "Q GLU 21": "OE1" <-> "OE2" Residue "Q ASP 40": "OD1" <-> "OD2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "X GLU 69": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "Y TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 52": "OD1" <-> "OD2" Residue "a TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "h PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 68": "OD1" <-> "OD2" Residue "o TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 152": "OE1" <-> "OE2" Residue "o GLU 188": "OE1" <-> "OE2" Residue "r GLU 9": "OE1" <-> "OE2" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r GLU 22": "OE1" <-> "OE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "v ASP 41": "OD1" <-> "OD2" Residue "v GLU 163": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 99257 Number of models: 1 Model: "" Number of chains: 49 Chain: "1" Number of atoms: 43202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2018, 43202 Classifications: {'RNA': 2018} Modifications used: {'rna2p_pur': 204, 'rna2p_pyr': 135, 'rna3p_pur': 932, 'rna3p_pyr': 747} Link IDs: {'rna2p': 338, 'rna3p': 1679} Chain breaks: 36 Chain: "2" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3102 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 11, 'rna3p_pur': 61, 'rna3p_pyr': 61} Link IDs: {'rna2p': 23, 'rna3p': 122} Chain breaks: 2 Chain: "3" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1015 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1015 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 12, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 311 Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2653 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2795 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 340} Chain: "D" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 408 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1126 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1745 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "G" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1452 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "K" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1145 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 705 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 323 Chain: "L" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 962 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "M" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1000 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} 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: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1483 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "P" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Chain: "Q" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1020 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 456 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "S" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1434 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "U" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 484 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 97} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 Chain: "V" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 976 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "W" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 948 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 323 Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 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: "Z" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 637 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 6, 'TRANS': 122} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 209 Chain: "a" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 1875 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 336} Link IDs: {'PTRANS': 16, 'TRANS': 361} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1211 Unresolved non-hydrogen angles: 1545 Unresolved non-hydrogen dihedrals: 996 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 15, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 26, 'PHE:plan': 14, 'GLU:plan': 18, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 627 Chain: "c" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 325 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "d" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 787 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Chain: "e" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} 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: "g" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 428 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 81} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 637 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "k" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 349 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 101 Chain: "m" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 2881 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'PTRANS': 34, 'TRANS': 449} Chain breaks: 6 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1068 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 924 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 11, 'HIS:plan': 14, 'PHE:plan': 12, 'GLU:plan': 10, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 556 Chain: "n" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 395} Chain breaks: 2 Chain: "o" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 897 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "p" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 1416 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1118 Unresolved non-hydrogen dihedrals: 730 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 9, 'ASP:plan': 22, 'PHE:plan': 10, 'GLU:plan': 8, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 448 Chain: "r" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1009 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "t" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1948 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain: "u" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 491 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 206 Chain: "v" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1143 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "y" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1107 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 614 Unresolved non-hydrogen angles: 802 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 335 Chain: "T" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 147 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "6" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1315 Classifications: {'RNA': 62} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 23, 'rna3p_pyr': 20} Link IDs: {'rna2p': 19, 'rna3p': 42} Chain breaks: 4 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 82647 SG CYS j 19 127.687 107.385 171.219 1.00 12.17 S ATOM 82675 SG CYS j 22 130.145 108.374 168.312 1.00 22.68 S ATOM 82771 SG CYS j 34 129.049 104.868 168.765 1.00 32.30 S ATOM 82788 SG CYS j 37 131.260 106.497 171.453 1.00 7.74 S Time building chain proxies: 42.09, per 1000 atoms: 0.42 Number of scatterers: 99257 At special positions: 0 Unit cell: (243.8, 180.2, 315.88, 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 113 16.00 P 2226 15.00 O 24792 8.00 N 18556 7.00 C 53569 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: 40.89 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " 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 37 " Number of angles added : 6 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13940 Finding SS restraints... Secondary structure from input PDB file: 259 helices and 89 sheets defined 39.1% alpha, 17.2% beta 645 base pairs and 1228 stacking pairs defined. Time for finding SS restraints: 30.70 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 removed outlier: 3.531A pdb=" N VAL 3 10 " --> pdb=" O VAL 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 97 removed outlier: 3.881A pdb=" N GLN 3 96 " --> pdb=" O GLN 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 104 through 121 Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 84 through 94 removed outlier: 4.343A pdb=" N GLU A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.519A pdb=" N THR A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 158' Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.602A pdb=" N VAL A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.599A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.501A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.567A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 removed outlier: 3.649A pdb=" N ARG C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.574A pdb=" N SER C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.880A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 4.134A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' 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 259 Processing helix chain 'C' and resid 259 through 264 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 322 through 334 Processing helix chain 'D' and resid 347 through 359 Processing helix chain 'D' and resid 474 through 483 Processing helix chain 'D' and resid 483 through 501 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.653A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 38 through 80 Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.579A pdb=" N ILE F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.098A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.135A pdb=" N VAL F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.589A pdb=" N VAL F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.182A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (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 228 through 232 Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.600A pdb=" N LEU G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 103 through 119 removed outlier: 3.619A pdb=" N LEU G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 111 " --> pdb=" O GLN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.693A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.056A pdb=" N LEU G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.951A 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 'G' and resid 228 through 232 Processing helix chain 'H' and resid 61 through 85 removed outlier: 3.908A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 94 through 106 removed outlier: 4.092A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 116 through 124 removed outlier: 3.845A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 136 Processing helix chain 'K' and resid 154 through 160 removed outlier: 3.792A pdb=" N PHE K 158 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.512A pdb=" N LEU L 33 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.719A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 93 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.620A pdb=" N LEU L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 104 removed outlier: 3.687A pdb=" N LYS M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 96 " --> pdb=" O TRP M 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU M 97 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M 104 " --> pdb=" O LYS M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 46 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 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.907A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 47 through 61 removed outlier: 3.800A pdb=" N TYR O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 101 removed outlier: 4.063A pdb=" N GLU O 101 " --> pdb=" O GLN O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.028A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 124 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 150 through 182 Processing helix chain 'O' and resid 188 through 195 Processing helix chain 'P' and resid 25 through 36 removed outlier: 3.570A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.635A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.515A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU P 103 " --> pdb=" O GLU P 99 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.601A pdb=" N ARG Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 53 Processing helix chain 'Q' and resid 63 through 72 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.600A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'S' and resid 32 through 49 removed outlier: 3.823A pdb=" N ILE S 47 " --> pdb=" O PHE S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'U' and resid 16 through 23 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 70 through 86 removed outlier: 3.740A pdb=" N PHE U 81 " --> pdb=" O LEU U 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'W' and resid 22 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.915A pdb=" N ASP W 59 " --> pdb=" O ARG W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.761A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU W 95 " --> pdb=" O LYS W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.822A pdb=" N VAL W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 205 removed outlier: 3.551A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 8 Processing helix chain 'X' and resid 12 through 16 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 79 removed outlier: 3.821A pdb=" N GLU X 76 " --> pdb=" O MET X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 103 Processing helix chain 'X' and resid 130 through 139 Processing helix chain 'Y' and resid 10 through 19 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 5.067A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 removed outlier: 3.695A pdb=" N GLN Y 41 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 121 removed outlier: 3.734A pdb=" N LEU Y 117 " --> pdb=" O ASP Y 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 Processing helix chain 'Z' and resid 89 through 93 Processing helix chain 'Z' and resid 97 through 103 Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 75 through 79 removed outlier: 4.210A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 75 through 79' Processing helix chain 'a' and resid 83 through 91 removed outlier: 3.617A pdb=" N ASP a 88 " --> pdb=" O ASN a 84 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS a 89 " --> pdb=" O GLU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 107 Processing helix chain 'a' and resid 130 through 140 removed outlier: 3.976A pdb=" N GLU a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS a 136 " --> pdb=" O ARG a 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 30 Processing helix chain 'b' and resid 39 through 69 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.716A pdb=" N TYR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 144 Processing helix chain 'b' and resid 145 through 161 Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 236 through 246 Processing helix chain 'b' and resid 264 through 275 Processing helix chain 'b' and resid 275 through 280 Processing helix chain 'b' and resid 328 through 341 Processing helix chain 'b' and resid 379 through 384 Processing helix chain 'b' and resid 399 through 407 Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 440 through 444 Processing helix chain 'b' and resid 448 through 465 removed outlier: 4.153A pdb=" N LEU b 454 " --> pdb=" O GLU b 450 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 50 Processing helix chain 'c' and resid 63 through 78 Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 48 removed outlier: 3.883A pdb=" N HIS d 48 " --> pdb=" O PHE d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 68 removed outlier: 4.109A pdb=" N ARG d 67 " --> pdb=" O GLU d 63 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY d 68 " --> pdb=" O VAL d 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 57 through 61 removed outlier: 3.674A pdb=" N ARG e 61 " --> pdb=" O LYS e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 75 through 80 removed outlier: 3.633A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 84 removed outlier: 3.850A pdb=" N MET e 84 " --> pdb=" O LEU e 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 81 through 84' Processing helix chain 'e' and resid 98 through 113 removed outlier: 3.506A pdb=" N GLU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 46 removed outlier: 4.284A pdb=" N TYR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.788A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 removed outlier: 3.667A pdb=" N ARG g 64 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 Processing helix chain 'g' and resid 81 through 106 Processing helix chain 'h' and resid 4 through 9 Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.749A pdb=" N GLN h 25 " --> pdb=" O GLN h 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU h 26 " --> pdb=" O GLU h 22 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU h 27 " --> pdb=" O LEU h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.159A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA h 54 " --> pdb=" O ARG h 50 " (cutoff:3.500A) 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 removed outlier: 3.638A pdb=" N GLU h 110 " --> pdb=" O GLN h 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.703A 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 95 removed outlier: 3.613A pdb=" N GLU i 86 " --> pdb=" O LYS i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 64 through 75 removed outlier: 3.562A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 Processing helix chain 'm' and resid 178 through 187 Processing helix chain 'm' and resid 221 through 225 Processing helix chain 'm' and resid 229 through 245 Processing helix chain 'm' and resid 249 through 260 Processing helix chain 'm' and resid 328 through 343 removed outlier: 3.745A pdb=" N TYR m 341 " --> pdb=" O CYS m 337 " (cutoff:3.500A) Processing helix chain 'm' and resid 483 through 495 removed outlier: 3.521A pdb=" N GLU m 492 " --> pdb=" O GLU m 488 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU m 493 " --> pdb=" O ALA m 489 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE m 494 " --> pdb=" O SER m 490 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 14 removed outlier: 3.744A pdb=" N ALA n 13 " --> pdb=" O ALA n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 40 Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 74 removed outlier: 4.154A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 98 removed outlier: 4.319A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS n 80 " --> pdb=" O PRO n 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG n 89 " --> pdb=" O LYS n 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 109 Processing helix chain 'n' and resid 115 through 123 Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 133 through 144 Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 215 through 241 removed outlier: 3.774A pdb=" N MET n 219 " --> pdb=" O ASP n 215 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA n 228 " --> pdb=" O GLU n 224 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY n 231 " --> pdb=" O GLN n 227 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE n 232 " --> pdb=" O ALA n 228 " (cutoff:3.500A) Processing helix chain 'n' and resid 250 through 255 Processing helix chain 'n' and resid 256 through 257 No H-bonds generated for 'chain 'n' and resid 256 through 257' Processing helix chain 'n' and resid 258 through 261 Processing helix chain 'n' and resid 365 through 375 removed outlier: 3.740A pdb=" N PHE n 371 " --> pdb=" O PHE n 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 384 through 387 Processing helix chain 'n' and resid 420 through 431 removed outlier: 4.204A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR n 425 " --> pdb=" O PRO n 421 " (cutoff:3.500A) Processing helix chain 'n' and resid 436 through 440 Processing helix chain 'n' and resid 554 through 558 Processing helix chain 'n' and resid 570 through 598 removed outlier: 4.361A pdb=" N SER n 574 " --> pdb=" O ARG n 570 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN n 578 " --> pdb=" O SER n 574 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU n 579 " --> pdb=" O LYS n 575 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN n 580 " --> pdb=" O LEU n 576 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN n 583 " --> pdb=" O GLU n 579 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN n 592 " --> pdb=" O ASN n 588 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 129 removed outlier: 4.860A pdb=" N GLN o 127 " --> pdb=" O MET o 123 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 164 removed outlier: 3.595A pdb=" N VAL o 162 " --> pdb=" O VAL o 158 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA o 163 " --> pdb=" O ALA o 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU o 164 " --> pdb=" O ASN o 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 182 through 186 removed outlier: 3.629A pdb=" N GLN o 185 " --> pdb=" O PRO o 182 " (cutoff:3.500A) Processing helix chain 'o' and resid 202 through 210 Processing helix chain 'r' and resid 5 through 15 removed outlier: 3.746A pdb=" N GLU r 9 " --> pdb=" O GLU r 5 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER r 10 " --> pdb=" O TYR r 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG r 12 " --> pdb=" O GLU r 8 " (cutoff:3.500A) Processing helix chain 'r' and resid 19 through 42 removed outlier: 5.178A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA r 39 " --> pdb=" O ALA r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 68 removed outlier: 3.614A pdb=" N GLU r 52 " --> pdb=" O LYS r 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS r 53 " --> pdb=" O LEU r 49 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 't' and resid 25 through 47 removed outlier: 3.558A pdb=" N ALA t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 76 removed outlier: 3.914A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE t 58 " --> pdb=" O ALA t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 112 removed outlier: 3.550A pdb=" N ARG t 110 " --> pdb=" O ARG t 106 " (cutoff:3.500A) Processing helix chain 't' and resid 126 through 136 Processing helix chain 't' and resid 146 through 158 Processing helix chain 't' and resid 171 through 180 removed outlier: 3.672A pdb=" N ILE t 175 " --> pdb=" O ASP t 171 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 183 No H-bonds generated for 'chain 't' and resid 181 through 183' Processing helix chain 't' and resid 186 through 197 Processing helix chain 't' and resid 200 through 207 Processing helix chain 't' and resid 239 through 249 removed outlier: 3.505A pdb=" N GLU t 243 " --> pdb=" O GLU t 239 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.836A pdb=" N ASN u 92 " --> pdb=" O ALA u 88 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 12 removed outlier: 3.808A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 138 through 152 Processing helix chain 'v' and resid 160 through 172 removed outlier: 3.659A pdb=" N LEU v 170 " --> pdb=" O TYR v 166 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 194 through 206 removed outlier: 3.733A pdb=" N LYS v 206 " --> pdb=" O TYR v 202 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.713A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 43 removed outlier: 4.099A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 52 through 56 removed outlier: 3.948A pdb=" N GLY y 55 " --> pdb=" O THR y 52 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 51 through 55 removed outlier: 3.624A pdb=" N THR 3 52 " --> pdb=" O TYR 3 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.382A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 194 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.382A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 232 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.441A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.441A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 84 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 203 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.367A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N HIS B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 74 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL B 57 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.367A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 17 through 23 removed outlier: 4.879A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 65 removed outlier: 4.446A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.549A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.882A pdb=" N TYR F 82 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 212 through 213 removed outlier: 3.959A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AB8, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC1, first strand: chain 'H' and resid 6 through 12 removed outlier: 3.644A pdb=" N GLU H 45 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 25 through 29 Processing sheet with id=AC3, first strand: chain 'H' and resid 130 through 135 removed outlier: 4.538A pdb=" N GLU H 141 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 91 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR H 178 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC5, first strand: chain 'K' and resid 198 through 205 removed outlier: 6.250A pdb=" N VAL K 53 " --> pdb=" O CYS K 203 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA K 237 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN K 253 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE K 239 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AC7, first strand: chain 'K' and resid 111 through 113 removed outlier: 7.111A pdb=" N ALA K 87 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K 166 " --> pdb=" O PHE K 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AC9, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD1, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.625A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE M 61 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU M 15 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR M 59 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.599A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 7 through 11 Processing sheet with id=AD4, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AD5, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.584A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Q' and resid 61 through 62 removed outlier: 3.765A pdb=" N LEU Q 105 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY Q 86 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE Q 107 " --> pdb=" O GLY Q 86 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL Q 88 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD9, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AE1, first strand: chain 'S' and resid 55 through 62 removed outlier: 7.172A pdb=" N VAL S 9 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE S 60 " --> pdb=" O GLN S 7 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN S 7 " --> pdb=" O ILE S 60 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU S 62 " --> pdb=" O GLU S 5 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU S 5 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG S 25 " --> pdb=" O VAL T 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 87 through 95 removed outlier: 6.549A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 51 through 53 removed outlier: 4.108A pdb=" N LEU U 103 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL U 100 " --> pdb=" O THR U 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 39 through 40 Processing sheet with id=AE5, first strand: chain 'V' and resid 24 through 27 removed outlier: 7.311A pdb=" N LEU V 36 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS V 65 " --> pdb=" O LEU V 36 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE V 38 " --> pdb=" O THR V 63 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR V 63 " --> pdb=" O ILE V 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE V 79 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 87 through 88 removed outlier: 6.319A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AE8, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE9, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.020A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF2, first strand: chain 'Y' and resid 78 through 81 removed outlier: 6.378A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 86 through 87 Processing sheet with id=AF4, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.458A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL Z 23 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ARG Z 48 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N LYS Z 21 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS Z 21 " --> pdb=" O ILE Z 13 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR Z 85 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU Z 12 " --> pdb=" O THR Z 83 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR Z 83 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.701A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.137A pdb=" N VAL a 124 " --> pdb=" O GLU a 145 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 207 through 212 removed outlier: 3.565A pdb=" N ALA b 250 " --> pdb=" O THR b 170 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 254 through 256 removed outlier: 5.890A pdb=" N LEU b 286 " --> pdb=" O VAL b 319 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 80 through 81 Processing sheet with id=AG1, first strand: chain 'd' and resid 54 through 56 removed outlier: 3.584A pdb=" N LYS d 83 " --> pdb=" O TYR d 93 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR d 14 " --> pdb=" O VAL d 111 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AG3, first strand: chain 'f' and resid 63 through 68 removed outlier: 4.936A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA f 81 " --> pdb=" O HIS f 76 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AG5, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG6, first strand: chain 'k' and resid 3 through 4 removed outlier: 3.728A pdb=" N THR k 45 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR k 66 " --> pdb=" O THR k 21 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'm' and resid 345 through 348 Processing sheet with id=AG8, first strand: chain 'm' and resid 386 through 391 Processing sheet with id=AG9, first strand: chain 'm' and resid 452 through 457 removed outlier: 3.520A pdb=" N SER m 454 " --> pdb=" O ALA m 469 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 533 through 536 Processing sheet with id=AH2, first strand: chain 'm' and resid 576 through 581 removed outlier: 4.375A pdb=" N TYR m 595 " --> pdb=" O THR m 592 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL m 596 " --> pdb=" O THR m 609 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR m 609 " --> pdb=" O VAL m 596 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE m 598 " --> pdb=" O VAL m 607 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 617 through 622 Processing sheet with id=AH4, first strand: chain 'm' and resid 662 through 665 removed outlier: 5.918A pdb=" N VAL m 681 " --> pdb=" O ILE m 703 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE m 703 " --> pdb=" O VAL m 681 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL m 683 " --> pdb=" O LEU m 701 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 715 through 720 removed outlier: 3.512A pdb=" N SER m 717 " --> pdb=" O ALA m 730 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AH7, first strand: chain 'n' and resid 177 through 183 removed outlier: 5.607A pdb=" N LEU n 177 " --> pdb=" O GLU n 192 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU n 192 " --> pdb=" O LEU n 177 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'n' and resid 248 through 249 removed outlier: 3.665A pdb=" N LYS n 248 " --> pdb=" O GLU n 264 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 379 through 382 Processing sheet with id=AI1, first strand: chain 'o' and resid 131 through 138 removed outlier: 5.138A pdb=" N VAL o 131 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU o 152 " --> pdb=" O VAL o 131 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG o 133 " --> pdb=" O PHE o 150 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE o 150 " --> pdb=" O ARG o 133 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG o 135 " --> pdb=" O TYR o 148 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N TYR o 148 " --> pdb=" O ARG o 135 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER o 137 " --> pdb=" O LYS o 146 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR o 108 " --> pdb=" O LYS o 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR o 169 " --> pdb=" O LEU o 176 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'p' and resid 96 through 102 removed outlier: 6.521A pdb=" N ILE p 430 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER p 100 " --> pdb=" O LEU p 428 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU p 428 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN p 427 " --> pdb=" O GLY p 423 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY p 423 " --> pdb=" O GLN p 427 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'p' and resid 107 through 112 removed outlier: 5.887A pdb=" N ALA p 126 " --> pdb=" O GLN p 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN p 138 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL p 128 " --> pdb=" O LYS p 136 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'p' and resid 146 through 151 removed outlier: 6.557A pdb=" N ALA p 161 " --> pdb=" O LYS p 147 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA p 149 " --> pdb=" O LEU p 159 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU p 159 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP p 151 " --> pdb=" O SER p 157 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER p 157 " --> pdb=" O TRP p 151 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS p 166 " --> pdb=" O SER p 162 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR p 191 " --> pdb=" O HIS p 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL p 171 " --> pdb=" O LEU p 189 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU p 189 " --> pdb=" O VAL p 171 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 202 through 203 removed outlier: 3.591A pdb=" N ILE p 263 " --> pdb=" O ILE p 223 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 272 through 277 removed outlier: 4.097A pdb=" N GLY p 288 " --> pdb=" O THR p 292 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR p 292 " --> pdb=" O GLY p 288 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP p 305 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP p 297 " --> pdb=" O ASN p 303 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASN p 303 " --> pdb=" O ASP p 297 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 313 through 319 removed outlier: 4.045A pdb=" N HIS p 333 " --> pdb=" O SER p 329 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'p' and resid 358 through 363 removed outlier: 4.060A pdb=" N THR p 379 " --> pdb=" O SER p 375 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL p 382 " --> pdb=" O TYR p 393 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'r' and resid 191 through 195 removed outlier: 3.987A pdb=" N ALA r 256 " --> pdb=" O ASN r 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN r 243 " --> pdb=" O LEU r 257 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU r 221 " --> pdb=" O VAL r 199 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL r 199 " --> pdb=" O GLU r 221 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 't' and resid 211 through 212 removed outlier: 4.796A pdb=" N ASN t 119 " --> pdb=" O ARG t 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG t 94 " --> pdb=" O ASN t 119 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL t 123 " --> pdb=" O LEU t 90 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 't' and resid 165 through 168 removed outlier: 3.968A pdb=" N ILE t 162 " --> pdb=" O GLN t 165 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE t 159 " --> pdb=" O TRP t 209 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AJ4, first strand: chain 'y' and resid 3 through 5 removed outlier: 5.994A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'y' and resid 18 through 19 removed outlier: 6.549A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AJ7, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AJ8, first strand: chain 'y' and resid 153 through 154 removed outlier: 6.288A pdb=" N ALA y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 2455 hydrogen bonds defined for protein. 6942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1545 hydrogen bonds 2484 hydrogen bond angles 0 basepair planarities 645 basepair parallelities 1228 stacking parallelities Total time for adding SS restraints: 105.14 Time building geometry restraints manager: 44.08 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: 12196 1.32 - 1.44: 40369 1.44 - 1.57: 48425 1.57 - 1.69: 4409 1.69 - 1.82: 185 Bond restraints: 105584 Sorted by residual: bond pdb=" CA PRO L 60 " pdb=" C PRO L 60 " ideal model delta sigma weight residual 1.514 1.479 0.035 5.50e-03 3.31e+04 4.09e+01 bond pdb=" CG GLN m 252 " pdb=" CD GLN m 252 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.34e+01 bond pdb=" CA PRO m 479 " pdb=" C PRO m 479 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.71e+01 bond pdb=" CG LEU R 15 " pdb=" CD2 LEU R 15 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" CG1 ILE S 78 " pdb=" CD1 ILE S 78 " ideal model delta sigma weight residual 1.513 1.382 0.131 3.90e-02 6.57e+02 1.13e+01 ... (remaining 105579 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.59: 5775 103.59 - 111.22: 53484 111.22 - 118.85: 39188 118.85 - 126.47: 48305 126.47 - 134.10: 6995 Bond angle restraints: 153747 Sorted by residual: angle pdb=" N ALA L 47 " pdb=" CA ALA L 47 " pdb=" C ALA L 47 " ideal model delta sigma weight residual 109.81 120.47 -10.66 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLN X 10 " pdb=" CA GLN X 10 " pdb=" C GLN X 10 " ideal model delta sigma weight residual 114.62 109.33 5.29 1.14e+00 7.69e-01 2.16e+01 angle pdb=" N TYR 3 99 " pdb=" CA TYR 3 99 " pdb=" C TYR 3 99 " ideal model delta sigma weight residual 113.01 107.46 5.55 1.20e+00 6.94e-01 2.14e+01 angle pdb=" CA GLU E 77 " pdb=" CB GLU E 77 " pdb=" CG GLU E 77 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CB MET X 72 " pdb=" CG MET X 72 " pdb=" SD MET X 72 " ideal model delta sigma weight residual 112.70 126.41 -13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 153742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 56222 35.94 - 71.89: 2079 71.89 - 107.83: 179 107.83 - 143.78: 23 143.78 - 179.72: 43 Dihedral angle restraints: 58546 sinusoidal: 37126 harmonic: 21420 Sorted by residual: dihedral pdb=" O4' U 1 3 " pdb=" C1' U 1 3 " pdb=" N1 U 1 3 " pdb=" C2 U 1 3 " ideal model delta sinusoidal sigma weight residual -160.00 19.72 -179.72 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual -160.00 19.49 -179.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 13407 " pdb=" C1' U 13407 " pdb=" N1 U 13407 " pdb=" C2 U 13407 " ideal model delta sinusoidal sigma weight residual 200.00 25.20 174.80 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 58543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 17600 0.060 - 0.120: 1625 0.120 - 0.179: 131 0.179 - 0.239: 15 0.239 - 0.299: 2 Chirality restraints: 19373 Sorted by residual: chirality pdb=" CG LEU O 56 " pdb=" CB LEU O 56 " pdb=" CD1 LEU O 56 " pdb=" CD2 LEU O 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ALA L 47 " pdb=" N ALA L 47 " pdb=" C ALA L 47 " pdb=" CB ALA L 47 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C2' C 13098 " pdb=" C3' C 13098 " pdb=" O2' C 13098 " pdb=" C1' C 13098 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 19370 not shown) Planarity restraints: 11532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE d 30 " -0.074 2.00e-02 2.50e+03 5.30e-02 4.92e+01 pdb=" CG PHE d 30 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE d 30 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE d 30 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE d 30 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE d 30 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE d 30 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR v 174 " -0.008 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR v 174 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR v 174 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR v 174 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR v 174 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR v 174 " -0.051 2.00e-02 2.50e+03 pdb=" CZ TYR v 174 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR v 174 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE O 109 " -0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+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 " -0.052 5.00e-02 4.00e+02 ... (remaining 11529 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 2183 2.63 - 3.20: 87992 3.20 - 3.77: 185541 3.77 - 4.33: 244931 4.33 - 4.90: 344449 Nonbonded interactions: 865096 Sorted by model distance: nonbonded pdb=" OG1 THR H 104 " pdb=" OE1 GLU H 105 " model vdw 2.066 2.440 nonbonded pdb=" N GLU Q 92 " pdb=" OE1 GLU Q 92 " model vdw 2.144 2.520 nonbonded pdb=" OD1 ASP M 33 " pdb=" N HIS M 34 " model vdw 2.151 2.520 nonbonded pdb=" O2' A 13318 " pdb=" OP2 G 13319 " model vdw 2.165 2.440 nonbonded pdb=" OP1 A 11424 " pdb=" O2' C 11425 " model vdw 2.173 2.440 ... (remaining 865091 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2226 5.49 5 S 113 5.16 5 C 53569 2.51 5 N 18556 2.21 5 O 24792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.390 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: 31.610 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.650 Process input model: 306.870 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 355.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 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 : 0.004 0.131 105584 Z= 0.230 Angle : 0.544 13.713 153747 Z= 0.287 Chirality : 0.035 0.299 19373 Planarity : 0.004 0.104 11532 Dihedral : 16.639 179.723 44606 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.31 (0.10), residues: 7220 helix: 0.52 (0.11), residues: 2557 sheet: -0.33 (0.16), residues: 1108 loop : -0.62 (0.11), residues: 3555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1450 time to evaluate : 5.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 1461 average time/residue: 1.0166 time to fit residues: 2412.8309 Evaluate side-chains 748 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 742 time to evaluate : 5.680 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.7229 time to fit residues: 14.9867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 792 optimal weight: 5.9990 chunk 710 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 242 optimal weight: 30.0000 chunk 479 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 735 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 447 optimal weight: 0.9980 chunk 547 optimal weight: 40.0000 chunk 851 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 2 GLN ** 3 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN C 198 ASN C 245 HIS F 45 GLN F 86 HIS F 247 GLN ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 122 HIS ** N 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS N 57 GLN O 51 ASN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS P 97 ASN Q 57 ASN ** Q 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 GLN S 146 HIS X 38 GLN X 84 HIS Y 18 HIS a 14 HIS e 85 HIS ** h 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 HIS n 580 ASN ** o 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 ASN t 63 GLN t 118 ASN ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 6 GLN v 10 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.147 105584 Z= 0.527 Angle : 0.921 23.408 153747 Z= 0.459 Chirality : 0.049 0.377 19373 Planarity : 0.008 0.135 11532 Dihedral : 16.102 179.755 34522 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.93 % Rotamer Outliers : 6.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.10), residues: 7220 helix: 0.48 (0.10), residues: 2567 sheet: -0.30 (0.16), residues: 1058 loop : -0.69 (0.10), residues: 3595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 794 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 285 outliers final: 133 residues processed: 1007 average time/residue: 0.9309 time to fit residues: 1575.5387 Evaluate side-chains 725 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 592 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 0.7420 time to fit residues: 189.2478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 473 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 708 optimal weight: 0.7980 chunk 580 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 853 optimal weight: 5.9990 chunk 921 optimal weight: 4.9990 chunk 759 optimal weight: 20.0000 chunk 846 optimal weight: 40.0000 chunk 290 optimal weight: 0.6980 chunk 684 optimal weight: 40.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN B 121 ASN B 319 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN L 40 GLN L 110 GLN M 81 GLN N 19 ASN N 57 GLN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 146 HIS ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN Y 54 GLN d 61 ASN ** h 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN m 301 ASN n 588 ASN ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 105584 Z= 0.324 Angle : 0.674 26.685 153747 Z= 0.340 Chirality : 0.040 0.332 19373 Planarity : 0.005 0.068 11532 Dihedral : 15.847 179.688 34522 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.48 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.19 (0.10), residues: 7220 helix: 0.80 (0.10), residues: 2565 sheet: -0.40 (0.16), residues: 1109 loop : -0.65 (0.11), residues: 3546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 673 time to evaluate : 5.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 65 residues processed: 769 average time/residue: 0.9942 time to fit residues: 1310.4223 Evaluate side-chains 637 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 572 time to evaluate : 5.794 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.7758 time to fit residues: 100.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 843 optimal weight: 10.0000 chunk 641 optimal weight: 50.0000 chunk 442 optimal weight: 0.7980 chunk 94 optimal weight: 30.0000 chunk 407 optimal weight: 50.0000 chunk 573 optimal weight: 20.0000 chunk 856 optimal weight: 8.9990 chunk 906 optimal weight: 4.9990 chunk 447 optimal weight: 0.7980 chunk 811 optimal weight: 9.9990 chunk 244 optimal weight: 50.0000 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 106 HIS B 293 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN F 45 GLN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 HIS ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN P 25 HIS ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 120 ASN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 61 ASN ** n 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 114 HIS ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 3 ASN v 23 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.117 105584 Z= 0.569 Angle : 0.900 35.884 153747 Z= 0.448 Chirality : 0.050 0.477 19373 Planarity : 0.007 0.141 11532 Dihedral : 16.401 179.883 34522 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.48 (0.10), residues: 7220 helix: 0.51 (0.10), residues: 2556 sheet: -0.51 (0.16), residues: 1114 loop : -0.80 (0.11), residues: 3550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 637 time to evaluate : 5.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 217 outliers final: 114 residues processed: 798 average time/residue: 0.9201 time to fit residues: 1250.2357 Evaluate side-chains 664 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 550 time to evaluate : 5.702 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.7247 time to fit residues: 160.8589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 755 optimal weight: 50.0000 chunk 514 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 675 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 773 optimal weight: 9.9990 chunk 626 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 462 optimal weight: 0.6980 chunk 813 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN C 162 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN L 103 ASN N 19 ASN O 43 ASN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 GLN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 ASN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 ASN ** h 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN m 301 ASN n 239 ASN ** o 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 248 GLN ** v 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 105584 Z= 0.258 Angle : 0.642 32.116 153747 Z= 0.325 Chirality : 0.039 0.289 19373 Planarity : 0.005 0.054 11532 Dihedral : 15.959 179.528 34522 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.20 (0.10), residues: 7220 helix: 0.85 (0.10), residues: 2577 sheet: -0.46 (0.16), residues: 1143 loop : -0.69 (0.11), residues: 3500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 609 time to evaluate : 5.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 46 residues processed: 674 average time/residue: 0.9366 time to fit residues: 1082.3220 Evaluate side-chains 614 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 568 time to evaluate : 5.774 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.7577 time to fit residues: 71.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 305 optimal weight: 0.0980 chunk 816 optimal weight: 0.0470 chunk 179 optimal weight: 10.0000 chunk 532 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 907 optimal weight: 8.9990 chunk 753 optimal weight: 20.0000 chunk 420 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 300 optimal weight: 0.6980 chunk 476 optimal weight: 5.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 47 ASN 3 78 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS N 156 HIS ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 HIS ** n 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 239 ASN o 177 GLN o 203 HIS ** t 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.086 105584 Z= 0.158 Angle : 0.571 26.580 153747 Z= 0.291 Chirality : 0.036 0.288 19373 Planarity : 0.004 0.050 11532 Dihedral : 15.652 179.945 34522 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.10), residues: 7220 helix: 1.10 (0.10), residues: 2586 sheet: -0.32 (0.16), residues: 1148 loop : -0.54 (0.11), residues: 3486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 645 time to evaluate : 6.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 683 average time/residue: 0.9417 time to fit residues: 1093.9735 Evaluate side-chains 602 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 575 time to evaluate : 5.861 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.8222 time to fit residues: 47.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 874 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 517 optimal weight: 10.0000 chunk 662 optimal weight: 7.9990 chunk 513 optimal weight: 9.9990 chunk 763 optimal weight: 30.0000 chunk 506 optimal weight: 8.9990 chunk 904 optimal weight: 0.9980 chunk 565 optimal weight: 8.9990 chunk 551 optimal weight: 0.0050 chunk 417 optimal weight: 0.0470 overall best weight: 2.8096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 47 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS P 64 ASN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 HIS ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 105584 Z= 0.333 Angle : 0.673 33.845 153747 Z= 0.338 Chirality : 0.041 0.280 19373 Planarity : 0.005 0.070 11532 Dihedral : 15.762 179.882 34522 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.15 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.02 (0.10), residues: 7220 helix: 1.04 (0.10), residues: 2588 sheet: -0.39 (0.15), residues: 1170 loop : -0.61 (0.11), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 574 time to evaluate : 5.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 44 residues processed: 616 average time/residue: 0.9950 time to fit residues: 1043.2610 Evaluate side-chains 582 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 538 time to evaluate : 5.816 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.7903 time to fit residues: 70.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 559 optimal weight: 5.9990 chunk 361 optimal weight: 0.0470 chunk 539 optimal weight: 40.0000 chunk 272 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 175 optimal weight: 40.0000 chunk 574 optimal weight: 0.8980 chunk 615 optimal weight: 20.0000 chunk 446 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 710 optimal weight: 4.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 47 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** m 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 HIS n 197 GLN ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN t 72 ASN ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 105584 Z= 0.244 Angle : 0.613 34.973 153747 Z= 0.309 Chirality : 0.038 0.338 19373 Planarity : 0.004 0.052 11532 Dihedral : 15.632 179.257 34522 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.07 (0.10), residues: 7220 helix: 1.12 (0.10), residues: 2584 sheet: -0.35 (0.15), residues: 1163 loop : -0.58 (0.11), residues: 3473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 569 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 599 average time/residue: 0.9468 time to fit residues: 971.8675 Evaluate side-chains 565 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 543 time to evaluate : 5.903 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.7456 time to fit residues: 38.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 822 optimal weight: 7.9990 chunk 866 optimal weight: 7.9990 chunk 790 optimal weight: 5.9990 chunk 842 optimal weight: 30.0000 chunk 865 optimal weight: 3.9990 chunk 507 optimal weight: 0.5980 chunk 367 optimal weight: 1.9990 chunk 661 optimal weight: 0.9990 chunk 258 optimal weight: 8.9990 chunk 761 optimal weight: 9.9990 chunk 796 optimal weight: 50.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 47 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 ASN n 74 HIS ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 203 HIS ** r 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 105584 Z= 0.321 Angle : 0.669 34.563 153747 Z= 0.336 Chirality : 0.040 0.378 19373 Planarity : 0.005 0.082 11532 Dihedral : 15.702 179.813 34522 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.00 (0.10), residues: 7220 helix: 1.02 (0.10), residues: 2604 sheet: -0.32 (0.16), residues: 1156 loop : -0.61 (0.11), residues: 3460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 562 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 593 average time/residue: 0.9467 time to fit residues: 960.8291 Evaluate side-chains 553 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 530 time to evaluate : 5.809 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.8236 time to fit residues: 41.6065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 839 optimal weight: 3.9990 chunk 553 optimal weight: 40.0000 chunk 890 optimal weight: 9.9990 chunk 543 optimal weight: 7.9990 chunk 422 optimal weight: 0.7980 chunk 619 optimal weight: 9.9990 chunk 934 optimal weight: 20.0000 chunk 860 optimal weight: 50.0000 chunk 744 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 574 optimal weight: 0.7980 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 ASN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 HIS n 74 HIS n 239 ASN ** n 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 ASN v 164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.113 105584 Z= 0.515 Angle : 0.831 37.175 153747 Z= 0.411 Chirality : 0.046 0.378 19373 Planarity : 0.007 0.149 11532 Dihedral : 16.101 179.173 34522 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.29 (0.10), residues: 7220 helix: 0.78 (0.10), residues: 2582 sheet: -0.42 (0.16), residues: 1142 loop : -0.79 (0.11), residues: 3496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14440 Ramachandran restraints generated. 7220 Oldfield, 0 Emsley, 7220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 551 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 563 average time/residue: 0.9492 time to fit residues: 905.7571 Evaluate side-chains 542 residues out of total 6385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 525 time to evaluate : 5.689 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.7440 time to fit residues: 30.4027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 938 random chunks: chunk 456 optimal weight: 0.9980 chunk 591 optimal weight: 7.9990 chunk 792 optimal weight: 40.0000 chunk 227 optimal weight: 50.0000 chunk 686 optimal weight: 30.0000 chunk 109 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 745 optimal weight: 20.0000 chunk 311 optimal weight: 0.7980 chunk 765 optimal weight: 30.0000 chunk 94 optimal weight: 40.0000 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN B 11 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN F 45 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 328 ASN n 74 HIS n 239 ASN ** n 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 203 HIS t 72 ASN t 100 ASN ** t 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 164 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.175830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.161609 restraints weight = 240801.373| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 1.32 r_work: 0.4022 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.7850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 105584 Z= 0.400 Angle : 0.731 37.683 153747 Z= 0.366 Chirality : 0.043 0.518 19373 Planarity : 0.006 0.104 11532 Dihedral : 15.989 179.655 34522 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.24 (0.10), residues: 7220 helix: 0.86 (0.10), residues: 2583 sheet: -0.46 (0.16), residues: 1143 loop : -0.77 (0.11), residues: 3494 =============================================================================== Job complete usr+sys time: 20998.17 seconds wall clock time: 372 minutes 13.15 seconds (22333.15 seconds total)