Starting phenix.real_space_refine on Tue Mar 19 20:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etc_24398/03_2024/8etc_24398.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2287 5.49 5 S 126 5.16 5 C 51235 2.51 5 N 17856 2.21 5 O 24146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "L ASP 148": "OD1" <-> "OD2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M ASP 33": "OD1" <-> "OD2" Residue "M PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N GLU 160": "OE1" <-> "OE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 49": "OD1" <-> "OD2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "R TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 95": "OD1" <-> "OD2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "S PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 70": "OD1" <-> "OD2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "V GLU 110": "OE1" <-> "OE2" Residue "X TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y GLU 82": "OE1" <-> "OE2" Residue "a GLU 85": "OE1" <-> "OE2" Residue "a GLU 119": "OE1" <-> "OE2" Residue "b PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 56": "OD1" <-> "OD2" Residue "b GLU 60": "OE1" <-> "OE2" Residue "b ASP 63": "OD1" <-> "OD2" Residue "b PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 112": "OD1" <-> "OD2" Residue "b TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 121": "OD1" <-> "OD2" Residue "b GLU 149": "OE1" <-> "OE2" Residue "b TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 448": "OE1" <-> "OE2" Residue "b GLU 450": "OE1" <-> "OE2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 107": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 104": "OE1" <-> "OE2" Residue "f GLU 34": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 87": "OD1" <-> "OD2" Residue "g GLU 96": "OE1" <-> "OE2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "i GLU 22": "OE1" <-> "OE2" Residue "i GLU 44": "OE1" <-> "OE2" Residue "k ASP 7": "OD1" <-> "OD2" Residue "r GLU 5": "OE1" <-> "OE2" Residue "r GLU 8": "OE1" <-> "OE2" Residue "r GLU 9": "OE1" <-> "OE2" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 243": "OE1" <-> "OE2" Residue "w PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 95651 Number of models: 1 Model: "" Number of chains: 43 Chain: "1" Number of atoms: 45843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2140, 45843 Classifications: {'RNA': 2140} Modifications used: {'rna2p_pur': 244, 'rna2p_pyr': 133, 'rna3p_pur': 972, 'rna3p_pyr': 791} Link IDs: {'rna2p': 376, 'rna3p': 1763} Chain breaks: 32 Chain: "2" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3131 Classifications: {'RNA': 147} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 64, 'rna3p_pyr': 59} Link IDs: {'rna2p': 24, 'rna3p': 122} Chain breaks: 2 Chain: "3" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "8" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 428 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "B" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2903 Classifications: {'peptide': 365} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 349} 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: "E" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1260 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "F" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1770 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "G" Number of atoms: 1453 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 182, 1437 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 182, 1437 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 bond proxies already assigned to first conformer: 1441 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: "L" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1427 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} 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: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 2 Chain: "Q" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1047 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 129} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1038 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 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: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1032 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain: "W" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1057 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "X" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} 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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 662 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 37 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: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2837 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 246 Chain: "c" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 477 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "d" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 849 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "e" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} 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: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 853 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} 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: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 754 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "j" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 72} Chain: "k" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "r" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1086 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Chain: "s" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "w" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3377 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 400} Chain breaks: 3 Chain: "y" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "T" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 159 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 4, 'TRANS': 16} 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 86761 SG CYS j 19 103.104 109.867 168.971 1.00 17.94 S ATOM 86789 SG CYS j 22 105.726 110.602 166.299 1.00 23.40 S ATOM 86885 SG CYS j 34 104.139 107.150 166.642 1.00 24.18 S ATOM 86902 SG CYS j 37 106.551 108.364 169.330 1.00 22.09 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASN G 182 " occ=0.56 ... (14 atoms not shown) pdb=" ND2BASN G 182 " occ=0.44 residue: pdb=" N AASP G 227 " occ=0.12 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.88 Time building chain proxies: 39.60, per 1000 atoms: 0.41 Number of scatterers: 95651 At special positions: 0 Unit cell: (217.3, 177.02, 257.58, 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 126 16.00 P 2287 15.00 O 24146 8.00 N 17856 7.00 C 51235 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: 39.77 Conformation dependent library (CDL) restraints added in 8.2 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 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " Number of angles added : 6 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11556 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 70 sheets defined 43.2% alpha, 14.6% beta 721 base pairs and 1293 stacking pairs defined. Time for finding SS restraints: 33.81 Creating SS restraints... Processing helix chain '3' and resid 3 through 11 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 103 No H-bonds generated for 'chain '3' and resid 101 through 103' Processing helix chain '3' and resid 104 through 119 Processing helix chain '8' and resid 6 through 20 removed outlier: 3.732A pdb=" N ASN 8 20 " --> pdb=" O ALA 8 16 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 30 removed outlier: 3.854A pdb=" N ARG 8 28 " --> pdb=" O PRO 8 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.539A 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 209 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.912A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.691A pdb=" N ARG C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 116 through 132 Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.559A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.568A pdb=" N VAL C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.856A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.735A 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 265 removed outlier: 4.321A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 34 through 80 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.947A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 172 through 180 removed outlier: 4.205A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 removed outlier: 3.622A pdb=" N SER F 184 " --> pdb=" O GLY F 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 209 removed outlier: 3.503A pdb=" N LEU F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.606A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 67 removed outlier: 3.674A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.782A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.490A 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: 4.122A pdb=" N LEU G 186 " --> pdb=" O AASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 223 removed outlier: 4.314A pdb=" N ASN G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.533A pdb=" N LYS G 232 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 removed outlier: 4.184A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 4.138A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.827A pdb=" N ALA L 130 " --> pdb=" O PRO L 127 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY L 131 " --> pdb=" O ARG L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 131' Processing helix chain 'L' and resid 148 through 153 removed outlier: 4.027A pdb=" N VAL L 152 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 173 Processing helix chain 'L' and resid 175 through 188 removed outlier: 3.802A pdb=" N LEU L 179 " --> pdb=" O ALA L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.484A pdb=" N GLN M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.953A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.688A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'O' and resid 16 through 31 Processing helix chain 'O' and resid 38 through 41 removed outlier: 3.740A pdb=" N GLU O 41 " --> pdb=" O ARG O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 38 through 41' Processing helix chain 'O' and resid 47 through 60 removed outlier: 3.592A pdb=" N ARG O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.151A 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 removed outlier: 3.809A pdb=" N SER O 144 " --> pdb=" O GLY O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 186 removed outlier: 4.054A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 removed outlier: 3.523A pdb=" N LEU O 192 " --> pdb=" O VAL O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.216A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 168 through 182 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 Processing helix chain 'Q' and resid 54 through 58 Processing helix chain 'Q' and resid 63 through 71 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 35 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 59 through 68 removed outlier: 3.588A pdb=" N ILE R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 112 removed outlier: 4.186A pdb=" N VAL R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG R 100 " --> pdb=" O MET R 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.761A pdb=" N THR R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 145 removed outlier: 3.532A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 144 Processing helix chain 'U' and resid 16 through 23 Processing helix chain 'U' and resid 26 through 38 Processing helix chain 'U' and resid 70 through 86 Processing helix chain 'V' and resid 68 through 72 Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 134 Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.657A 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: 3.895A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.915A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 204 removed outlier: 3.725A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 79 removed outlier: 3.526A pdb=" N GLU X 76 " --> pdb=" O MET X 72 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN X 79 " --> pdb=" O ILE X 75 " (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 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.965A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 76 No H-bonds generated for 'chain 'Y' and resid 74 through 76' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Z' and resid 58 through 67 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 7 through 12 Processing helix chain 'a' and resid 77 through 82 removed outlier: 3.962A pdb=" N LEU a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 132 through 141 Processing helix chain 'b' and resid 5 through 9 removed outlier: 4.070A pdb=" N ASN b 8 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE b 9 " --> pdb=" O PHE b 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5 through 9' Processing helix chain 'b' and resid 14 through 30 Processing helix chain 'b' and resid 39 through 69 removed outlier: 3.529A pdb=" N LYS b 50 " --> pdb=" O PHE b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 88 through 118 removed outlier: 3.521A pdb=" N LYS b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 143 removed outlier: 3.553A pdb=" N ARG b 143 " --> pdb=" O THR b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 161 removed outlier: 3.592A pdb=" N ARG b 160 " --> pdb=" O GLN b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.803A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 280 Proline residue: b 277 - end of helix Processing helix chain 'b' and resid 306 through 312 removed outlier: 3.731A pdb=" N ILE b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 379 through 384 removed outlier: 3.581A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR b 384 " --> pdb=" O ASP b 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 379 through 384' Processing helix chain 'b' and resid 398 through 406 Processing helix chain 'b' and resid 415 through 420 removed outlier: 3.971A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 430 removed outlier: 3.818A pdb=" N TYR b 429 " --> pdb=" O SER b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 442 through 445 Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.509A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 22 through 35 Processing helix chain 'c' and resid 40 through 51 Processing helix chain 'c' and resid 63 through 78 Processing helix chain 'c' and resid 87 through 96 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 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 37 through 42 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 46 removed outlier: 4.197A pdb=" N PHE f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.739A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 Processing helix chain 'g' and resid 66 through 71 Processing helix chain 'g' and resid 81 through 107 Processing helix chain 'h' and resid 4 through 10 Processing helix chain 'h' and resid 12 through 37 Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.097A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 27 Processing helix chain 'i' and resid 32 through 47 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 96 Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.737A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 75 Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 removed outlier: 3.529A pdb=" N ARG k 58 " --> pdb=" O ALA k 54 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER k 60 " --> pdb=" O LYS k 56 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.368A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 removed outlier: 3.539A pdb=" N ARG r 71 " --> pdb=" O GLN r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 removed outlier: 3.694A pdb=" N THR r 209 " --> pdb=" O SER r 205 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN r 210 " --> pdb=" O PRO r 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU r 211 " --> pdb=" O THR r 207 " (cutoff:3.500A) Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 31 removed outlier: 3.887A pdb=" N GLU s 20 " --> pdb=" O ARG s 16 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU s 25 " --> pdb=" O LYS s 21 " (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 59 Processing helix chain 'u' and resid 67 through 71 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.705A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA u 114 " --> pdb=" O LYS u 110 " (cutoff:3.500A) Processing helix chain 'w' and resid 15 through 24 Processing helix chain 'w' and resid 27 through 41 removed outlier: 3.996A pdb=" N PHE w 31 " --> pdb=" O SER w 27 " (cutoff:3.500A) Processing helix chain 'w' and resid 57 through 67 Processing helix chain 'w' and resid 96 through 108 Processing helix chain 'w' and resid 126 through 148 removed outlier: 3.570A pdb=" N GLN w 136 " --> pdb=" O TYR w 132 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU w 137 " --> pdb=" O GLY w 133 " (cutoff:3.500A) Processing helix chain 'w' and resid 164 through 175 Processing helix chain 'w' and resid 208 through 213 Processing helix chain 'w' and resid 213 through 218 removed outlier: 3.740A pdb=" N VAL w 217 " --> pdb=" O ASP w 213 " (cutoff:3.500A) Processing helix chain 'w' and resid 227 through 234 removed outlier: 4.207A pdb=" N LYS w 231 " --> pdb=" O ASN w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 264 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 292 Processing helix chain 'w' and resid 296 through 305 removed outlier: 3.545A pdb=" N ASP w 305 " --> pdb=" O LEU w 301 " (cutoff:3.500A) Processing helix chain 'w' and resid 310 through 329 Processing helix chain 'w' and resid 456 through 471 Processing helix chain 'w' and resid 639 through 646 Processing helix chain 'w' and resid 660 through 670 removed outlier: 4.783A pdb=" N GLU w 666 " --> pdb=" O TRP w 662 " (cutoff:3.500A) Processing helix chain 'w' and resid 762 through 766 Processing helix chain 'w' and resid 786 through 796 removed outlier: 3.700A pdb=" N ALA w 792 " --> pdb=" O LYS w 788 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 16 removed outlier: 4.237A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.568A pdb=" N GLU y 41 " --> pdb=" O VAL y 37 " (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 107 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 223 Processing helix chain 'z' and resid 88 through 101 removed outlier: 3.548A pdb=" N LYS z 101 " --> pdb=" O LYS z 97 " (cutoff:3.500A) Processing helix chain 'z' and resid 104 through 117 removed outlier: 3.501A pdb=" N PHE z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) 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 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.477A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.970A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.970A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 11 removed outlier: 7.218A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.561A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.395A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 97 removed outlier: 4.735A pdb=" N GLY E 84 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.723A pdb=" N VAL F 84 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 212 through 213 removed outlier: 4.091A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AB8, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.567A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 130 through 135 removed outlier: 4.650A pdb=" N GLU H 141 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG H 87 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG H 182 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR H 178 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC3, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.332A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 126 removed outlier: 4.756A pdb=" N LYS h 117 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 164 through 165 Processing sheet with id=AC7, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.607A pdb=" N GLN M 49 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR M 59 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 36 through 38 removed outlier: 6.004A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.243A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL O 34 " --> pdb=" O GLN O 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AD2, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.691A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD4, first strand: chain 'P' and resid 128 through 129 Processing sheet with id=AD5, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.213A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD7, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD8, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.113A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 87 through 95 removed outlier: 6.567A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 51 through 53 removed outlier: 4.497A pdb=" N LEU U 103 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL U 100 " --> pdb=" O THR U 96 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR U 96 " --> pdb=" O VAL U 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 39 through 40 removed outlier: 3.527A pdb=" N VAL U 40 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AE4, first strand: chain 'V' and resid 24 through 27 removed outlier: 5.503A pdb=" N ILE V 38 " --> pdb=" O THR V 63 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR V 63 " --> pdb=" O ILE V 38 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER V 40 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL V 80 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL V 103 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 87 through 88 removed outlier: 6.139A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.064A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE8, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.231A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF1, first strand: chain 'Y' and resid 98 through 99 removed outlier: 6.117A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 85 through 87 Processing sheet with id=AF3, first strand: chain 'Z' and resid 69 through 75 removed outlier: 6.749A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL Z 23 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.281A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 100 through 102 removed outlier: 3.879A pdb=" N THR a 126 " --> pdb=" O GLU a 145 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 206 through 212 removed outlier: 3.508A pdb=" N ILE b 220 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR b 170 " --> pdb=" O ALA b 250 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 254 through 256 removed outlier: 6.404A pdb=" N MET b 255 " --> pdb=" O ASN b 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AF9, first strand: chain 'c' and resid 37 through 38 removed outlier: 3.727A pdb=" N LEU c 55 " --> pdb=" O VAL c 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 54 through 56 removed outlier: 6.594A pdb=" N ARG d 55 " --> pdb=" O VAL d 96 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ALA d 98 " --> pdb=" O ARG d 55 " (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 9 through 19 removed outlier: 5.760A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG f 74 " --> pdb=" O ARG f 83 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (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 18 Processing sheet with id=AG6, first strand: chain 'k' and resid 43 through 48 removed outlier: 3.663A pdb=" N VAL k 33 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'r' and resid 180 through 184 removed outlier: 7.031A pdb=" N VAL r 219 " --> pdb=" O LYS r 200 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ALA r 256 " --> pdb=" O LYS r 180 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN r 182 " --> pdb=" O ALA r 256 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU r 258 " --> pdb=" O ASN r 182 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR r 184 " --> pdb=" O LEU r 258 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AG9, first strand: chain 'w' and resid 87 through 91 removed outlier: 6.346A pdb=" N VAL w 48 " --> pdb=" O VAL w 114 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU w 116 " --> pdb=" O VAL w 48 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE w 50 " --> pdb=" O LEU w 116 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP w 113 " --> pdb=" O THR w 154 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL w 156 " --> pdb=" O ASP w 113 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL w 115 " --> pdb=" O VAL w 156 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LYS w 158 " --> pdb=" O VAL w 115 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N HIS w 117 " --> pdb=" O LYS w 158 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N PHE w 160 " --> pdb=" O HIS w 117 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY w 153 " --> pdb=" O GLY w 200 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS w 198 " --> pdb=" O VAL w 179 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL w 179 " --> pdb=" O CYS w 198 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY w 200 " --> pdb=" O ASN w 177 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'w' and resid 255 through 257 Processing sheet with id=AH2, first strand: chain 'w' and resid 757 through 760 removed outlier: 5.997A pdb=" N THR w 757 " --> pdb=" O LYS w 780 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL w 782 " --> pdb=" O THR w 757 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL w 759 " --> pdb=" O VAL w 782 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'y' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.611A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'y' and resid 69 through 72 Processing sheet with id=AH6, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AH7, first strand: chain 'y' and resid 153 through 154 2065 hydrogen bonds defined for protein. 5934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1762 hydrogen bonds 2842 hydrogen bond angles 0 basepair planarities 721 basepair parallelities 1293 stacking parallelities Total time for adding SS restraints: 111.09 Time building geometry restraints manager: 42.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17507 1.33 - 1.45: 35972 1.45 - 1.57: 44004 1.57 - 1.69: 4542 1.69 - 1.81: 196 Bond restraints: 102221 Sorted by residual: bond pdb=" CA SER C 345 " pdb=" C SER C 345 " ideal model delta sigma weight residual 1.519 1.489 0.030 1.01e-02 9.80e+03 9.03e+00 bond pdb=" C ALA E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.24e-02 6.50e+03 6.70e+00 bond pdb=" CB LYS C 347 " pdb=" CG LYS C 347 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.53e+00 bond pdb=" CB MET u 94 " pdb=" CG MET u 94 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.52e+00 bond pdb=" CG TRP b 427 " pdb=" CD2 TRP b 427 " ideal model delta sigma weight residual 1.433 1.395 0.038 1.80e-02 3.09e+03 4.46e+00 ... (remaining 102216 not shown) Histogram of bond angle deviations from ideal: 93.44 - 101.56: 1766 101.56 - 109.69: 33312 109.69 - 117.81: 56184 117.81 - 125.94: 49315 125.94 - 134.06: 8655 Bond angle restraints: 149232 Sorted by residual: angle pdb=" N SER C 345 " pdb=" CA SER C 345 " pdb=" C SER C 345 " ideal model delta sigma weight residual 112.72 104.40 8.32 1.28e+00 6.10e-01 4.22e+01 angle pdb=" CA PRO b 162 " pdb=" N PRO b 162 " pdb=" CD PRO b 162 " ideal model delta sigma weight residual 112.00 104.74 7.26 1.40e+00 5.10e-01 2.69e+01 angle pdb=" C ILE g 95 " pdb=" N GLU g 96 " pdb=" CA GLU g 96 " ideal model delta sigma weight residual 120.68 112.18 8.50 1.70e+00 3.46e-01 2.50e+01 angle pdb=" O3' U 13328 " pdb=" C3' U 13328 " pdb=" C2' U 13328 " ideal model delta sigma weight residual 109.50 116.80 -7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA GLU g 96 " pdb=" CB GLU g 96 " pdb=" CG GLU g 96 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 ... (remaining 149227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 58101 35.93 - 71.86: 5670 71.86 - 107.79: 628 107.79 - 143.72: 24 143.72 - 179.65: 35 Dihedral angle restraints: 64458 sinusoidal: 46665 harmonic: 17793 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 18.93 -178.93 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 200.00 21.37 178.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 13084 " pdb=" C1' U 13084 " pdb=" N1 U 13084 " pdb=" C2 U 13084 " ideal model delta sinusoidal sigma weight residual 200.00 21.75 178.25 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 64455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 17881 0.084 - 0.169: 723 0.169 - 0.253: 21 0.253 - 0.337: 0 0.337 - 0.421: 2 Chirality restraints: 18627 Sorted by residual: chirality pdb=" CG LEU u 69 " pdb=" CB LEU u 69 " pdb=" CD1 LEU u 69 " pdb=" CD2 LEU u 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C3' U 13328 " pdb=" C4' U 13328 " pdb=" O3' U 13328 " pdb=" C2' U 13328 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU b 398 " pdb=" CB LEU b 398 " pdb=" CD1 LEU b 398 " pdb=" CD2 LEU b 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 18624 not shown) Planarity restraints: 10522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU b 161 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO b 162 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO b 162 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO b 162 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR b 10 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO b 11 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO b 11 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO b 11 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 39 " 0.056 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO B 40 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " 0.047 5.00e-02 4.00e+02 ... (remaining 10519 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1989 2.63 - 3.20: 81831 3.20 - 3.77: 182733 3.77 - 4.33: 244950 4.33 - 4.90: 339722 Nonbonded interactions: 851225 Sorted by model distance: nonbonded pdb=" O ASP M 82 " pdb=" OD1 ASP M 82 " model vdw 2.067 3.040 nonbonded pdb=" O ARG r 71 " pdb=" NH1 ARG r 71 " model vdw 2.074 2.520 nonbonded pdb=" O ASN B 212 " pdb=" ND2 ASN B 212 " model vdw 2.145 2.520 nonbonded pdb=" O2' C 13024 " pdb=" O5' A 13025 " model vdw 2.159 2.440 nonbonded pdb=" O2' G 11783 " pdb=" O2 U 11784 " model vdw 2.162 2.440 ... (remaining 851220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.12 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: 6.300 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: 0.100 Extract box with map and model: 28.790 Check model and map are aligned: 1.130 Set scattering table: 0.700 Process input model: 316.380 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 359.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.002 0.103 102221 Z= 0.154 Angle : 0.535 10.734 149232 Z= 0.283 Chirality : 0.033 0.421 18627 Planarity : 0.005 0.107 10522 Dihedral : 22.405 179.653 52902 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.93 % Favored : 95.87 % Rotamer: Outliers : 0.70 % Allowed : 8.98 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.30 (0.11), residues: 6010 helix: 0.51 (0.11), residues: 2352 sheet: -0.25 (0.18), residues: 804 loop : -0.70 (0.12), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP z 94 HIS 0.007 0.001 HIS H 59 PHE 0.053 0.002 PHE w 653 TYR 0.047 0.002 TYR b 388 ARG 0.024 0.001 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1439 time to evaluate : 5.651 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 revert: symmetry clash revert: symmetry clash REVERT: 3 40 ARG cc_start: 0.1115 (ptt-90) cc_final: 0.0455 (ttp80) REVERT: 8 39 MET cc_start: 0.1387 (ptp) cc_final: -0.1260 (ppp) REVERT: C 114 LYS cc_start: 0.8403 (tptp) cc_final: 0.8114 (ttmt) REVERT: C 270 VAL cc_start: 0.7406 (p) cc_final: 0.7132 (p) REVERT: C 296 ASP cc_start: 0.8048 (t70) cc_final: 0.7842 (t0) REVERT: F 172 ASP cc_start: 0.7824 (t0) cc_final: 0.7484 (t0) REVERT: G 231 ARG cc_start: 0.2904 (mtm180) cc_final: 0.1676 (mmp80) REVERT: H 8 ASP cc_start: 0.7123 (t0) cc_final: 0.6856 (t0) REVERT: H 88 TYR cc_start: 0.5316 (m-10) cc_final: 0.4593 (m-80) REVERT: H 135 SER cc_start: 0.6730 (p) cc_final: 0.3322 (p) REVERT: Q 72 ARG cc_start: 0.5147 (tpt170) cc_final: 0.4028 (tpt170) REVERT: R 89 MET cc_start: -0.3152 (pmm) cc_final: -0.3857 (mmp) REVERT: R 101 VAL cc_start: 0.8428 (m) cc_final: 0.8110 (p) REVERT: S 17 HIS cc_start: 0.8024 (m90) cc_final: 0.7294 (m90) REVERT: S 136 ARG cc_start: 0.5251 (mmt180) cc_final: 0.4836 (mpt180) REVERT: a 6 SER cc_start: 0.8188 (p) cc_final: 0.7924 (t) REVERT: a 9 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7263 (mmm160) REVERT: b 420 TYR cc_start: 0.3361 (m-10) cc_final: 0.2792 (m-80) REVERT: d 69 ILE cc_start: 0.5355 (tt) cc_final: 0.4780 (tt) REVERT: e 8 LYS cc_start: 0.6870 (mmtm) cc_final: 0.6463 (mtmt) REVERT: e 83 LEU cc_start: 0.7346 (tt) cc_final: 0.7108 (tp) REVERT: j 10 MET cc_start: 0.2944 (ptp) cc_final: -0.0063 (mmm) REVERT: w 646 GLU cc_start: 0.4715 (pm20) cc_final: 0.4361 (tm-30) REVERT: w 769 LYS cc_start: 0.4696 (tmtt) cc_final: 0.2935 (pttp) outliers start: 29 outliers final: 6 residues processed: 1458 average time/residue: 1.0693 time to fit residues: 2533.6773 Evaluate side-chains 762 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 756 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain b residue 458 GLU Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain y residue 145 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 694 optimal weight: 2.9990 chunk 623 optimal weight: 20.0000 chunk 345 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 420 optimal weight: 0.0870 chunk 332 optimal weight: 0.7980 chunk 644 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 chunk 391 optimal weight: 0.5980 chunk 479 optimal weight: 0.8980 chunk 746 optimal weight: 6.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 117 GLN 8 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 182 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 331 ASN E 75 GLN E 157 GLN F 100 ASN F 120 ASN G 137 ASN L 28 GLN L 110 GLN M 49 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 HIS Y 41 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 156 GLN ** f 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN h 15 ASN h 25 GLN j 48 ASN ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN r 72 ASN ** u 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 291 ASN w 671 ASN y 6 GLN y 145 ASN y 178 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 102221 Z= 0.222 Angle : 0.631 14.282 149232 Z= 0.321 Chirality : 0.037 0.272 18627 Planarity : 0.005 0.083 10522 Dihedral : 23.158 179.933 41963 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 3.49 % Allowed : 16.30 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.05 (0.11), residues: 6010 helix: 0.78 (0.11), residues: 2351 sheet: -0.19 (0.18), residues: 809 loop : -0.59 (0.12), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 358 HIS 0.021 0.002 HIS S 17 PHE 0.039 0.003 PHE b 69 TYR 0.029 0.002 TYR G 226 ARG 0.022 0.001 ARG y 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 845 time to evaluate : 5.742 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: 3 27 PHE cc_start: 0.5894 (m-80) cc_final: 0.5347 (m-80) REVERT: 3 40 ARG cc_start: 0.1686 (ptt180) cc_final: 0.0721 (ttp-170) REVERT: 8 39 MET cc_start: 0.1438 (ptp) cc_final: -0.1397 (ppp) REVERT: C 114 LYS cc_start: 0.8574 (tptp) cc_final: 0.8204 (ttmt) REVERT: C 296 ASP cc_start: 0.8119 (t70) cc_final: 0.7912 (t0) REVERT: F 172 ASP cc_start: 0.7735 (t0) cc_final: 0.7463 (t0) REVERT: G 84 LYS cc_start: 0.6475 (tptt) cc_final: 0.6163 (mtpt) REVERT: G 231 ARG cc_start: 0.3280 (mtm180) cc_final: 0.1977 (mmp80) REVERT: H 8 ASP cc_start: 0.7232 (t0) cc_final: 0.6805 (t0) REVERT: L 67 MET cc_start: 0.8549 (pmm) cc_final: 0.8299 (pmm) REVERT: L 88 ARG cc_start: 0.6849 (mpt180) cc_final: 0.6642 (mpt90) REVERT: Q 72 ARG cc_start: 0.5008 (tpt170) cc_final: 0.4110 (tpt170) REVERT: R 89 MET cc_start: -0.3391 (pmm) cc_final: -0.3644 (mmp) REVERT: X 133 ASP cc_start: 0.7915 (t0) cc_final: 0.7288 (t0) REVERT: a 9 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7383 (mmt180) REVERT: b 7 LYS cc_start: 0.5168 (tmtt) cc_final: 0.4760 (tmtt) REVERT: h 22 GLU cc_start: 0.7423 (pp20) cc_final: 0.7072 (mt-10) REVERT: h 23 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8413 (mm) REVERT: h 80 LEU cc_start: 0.8064 (mt) cc_final: 0.7680 (mt) REVERT: j 10 MET cc_start: 0.2933 (ptp) cc_final: -0.0218 (mmm) REVERT: r 41 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7219 (mtpp) REVERT: r 51 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5402 (mm-40) REVERT: u 107 LEU cc_start: 0.6414 (pp) cc_final: 0.5804 (pp) REVERT: w 646 GLU cc_start: 0.5180 (pm20) cc_final: 0.4109 (tm-30) REVERT: w 769 LYS cc_start: 0.4963 (tmtt) cc_final: 0.3062 (pttm) REVERT: y 93 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6667 (ptpp) REVERT: T 151 LEU cc_start: 0.7875 (mm) cc_final: 0.7669 (mm) outliers start: 156 outliers final: 74 residues processed: 945 average time/residue: 0.9285 time to fit residues: 1483.4287 Evaluate side-chains 762 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 685 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 45 PHE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain P residue 139 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain b residue 18 PHE Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain f residue 34 GLU Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain k residue 64 ASP Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 51 GLN Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 122 ASN Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 93 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 414 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 621 optimal weight: 7.9990 chunk 508 optimal weight: 0.0470 chunk 205 optimal weight: 10.0000 chunk 747 optimal weight: 8.9990 chunk 807 optimal weight: 10.0000 chunk 665 optimal weight: 0.7980 chunk 741 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 599 optimal weight: 1.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 120 ASN H 64 HIS H 77 ASN N 57 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 190 GLN P 50 ASN P 54 HIS ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 GLN S 153 HIS ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 HIS ** Y 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 139 GLN b 413 ASN f 25 HIS ** f 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS r 72 ASN ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 134 GLN w 291 ASN w 671 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 102221 Z= 0.222 Angle : 0.593 11.962 149232 Z= 0.302 Chirality : 0.036 0.251 18627 Planarity : 0.005 0.080 10522 Dihedral : 23.036 179.219 41948 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 3.65 % Allowed : 18.27 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 (0.11), residues: 6010 helix: 0.73 (0.11), residues: 2369 sheet: -0.19 (0.18), residues: 817 loop : -0.59 (0.12), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP M 78 HIS 0.047 0.002 HIS b 104 PHE 0.033 0.002 PHE b 69 TYR 0.034 0.002 TYR E 177 ARG 0.022 0.001 ARG b 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 771 time to evaluate : 5.541 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: 3 27 PHE cc_start: 0.6671 (m-80) cc_final: 0.5885 (m-80) REVERT: 3 82 LEU cc_start: 0.5242 (mm) cc_final: 0.4878 (mm) REVERT: 8 39 MET cc_start: 0.1935 (ptp) cc_final: -0.1397 (ppp) REVERT: C 114 LYS cc_start: 0.8585 (tptp) cc_final: 0.8072 (ttmt) REVERT: E 177 TYR cc_start: 0.6720 (t80) cc_final: 0.6506 (t80) REVERT: G 84 LYS cc_start: 0.6977 (tptt) cc_final: 0.6733 (pttt) REVERT: G 231 ARG cc_start: 0.3415 (mtm180) cc_final: 0.1991 (mmp80) REVERT: H 8 ASP cc_start: 0.7363 (t0) cc_final: 0.6977 (t0) REVERT: L 67 MET cc_start: 0.8679 (pmm) cc_final: 0.8423 (pmm) REVERT: L 88 ARG cc_start: 0.7312 (mpt180) cc_final: 0.7102 (mpt90) REVERT: N 67 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: Q 72 ARG cc_start: 0.4972 (tpt170) cc_final: 0.3866 (tpt170) REVERT: R 89 MET cc_start: -0.3062 (pmm) cc_final: -0.3472 (mmp) REVERT: S 43 PHE cc_start: 0.4981 (OUTLIER) cc_final: 0.4764 (m-10) REVERT: X 38 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6000 (mt0) REVERT: X 116 ASN cc_start: 0.5109 (p0) cc_final: 0.4804 (p0) REVERT: b 144 GLN cc_start: 0.5661 (mp10) cc_final: 0.5342 (mp10) REVERT: h 23 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8475 (mm) REVERT: h 109 LYS cc_start: 0.8062 (tptp) cc_final: 0.7686 (ttpt) REVERT: i 41 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8058 (tt) REVERT: j 10 MET cc_start: 0.3088 (ptp) cc_final: -0.0443 (mmm) REVERT: j 57 ARG cc_start: 0.6743 (ptp90) cc_final: 0.6488 (ptp90) REVERT: s 9 LYS cc_start: 0.5686 (tptt) cc_final: 0.4924 (ttmt) REVERT: u 2 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5489 (tpt90) REVERT: w 646 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.4216 (tm-30) REVERT: y 93 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6454 (ptpp) REVERT: y 162 HIS cc_start: 0.4705 (OUTLIER) cc_final: 0.4420 (m90) outliers start: 164 outliers final: 88 residues processed: 876 average time/residue: 0.9222 time to fit residues: 1373.4745 Evaluate side-chains 766 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 670 time to evaluate : 5.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain b residue 61 LYS Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 GLN Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 68 HIS Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain u residue 2 ARG Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 93 LYS Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain y residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 738 optimal weight: 7.9990 chunk 562 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 356 optimal weight: 0.9990 chunk 502 optimal weight: 10.0000 chunk 750 optimal weight: 6.9990 chunk 794 optimal weight: 5.9990 chunk 392 optimal weight: 1.9990 chunk 711 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 106 HIS 8 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN E 75 GLN F 86 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN A H 96 HIS ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 GLN S 87 HIS S 153 HIS V 49 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN Y 18 HIS ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 125 GLN a 139 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 HIS ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** u 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 HIS w 671 ASN ** y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 102221 Z= 0.366 Angle : 0.724 14.828 149232 Z= 0.367 Chirality : 0.042 0.298 18627 Planarity : 0.006 0.098 10522 Dihedral : 23.098 179.630 41948 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 4.88 % Allowed : 19.31 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6010 helix: 0.50 (0.10), residues: 2369 sheet: -0.26 (0.18), residues: 815 loop : -0.73 (0.12), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP M 78 HIS 0.032 0.002 HIS r 68 PHE 0.027 0.002 PHE b 69 TYR 0.043 0.003 TYR C 333 ARG 0.021 0.001 ARG V 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 716 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 3 GLN cc_start: 0.4798 (OUTLIER) cc_final: 0.4562 (tm-30) REVERT: 8 39 MET cc_start: 0.2689 (ptp) cc_final: -0.0590 (ppp) REVERT: B 214 MET cc_start: 0.6826 (mmm) cc_final: 0.6620 (mmm) REVERT: C 56 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6242 (pt0) REVERT: C 76 ILE cc_start: 0.6945 (tp) cc_final: 0.6727 (mp) REVERT: G 52 TRP cc_start: 0.6214 (m100) cc_final: 0.5791 (m-10) REVERT: H 8 ASP cc_start: 0.7216 (t0) cc_final: 0.6995 (t0) REVERT: N 34 ASN cc_start: 0.8588 (m-40) cc_final: 0.8383 (t0) REVERT: P 75 GLU cc_start: 0.7571 (pt0) cc_final: 0.7349 (pt0) REVERT: R 89 MET cc_start: -0.2808 (pmm) cc_final: -0.3393 (mmp) REVERT: S 89 MET cc_start: 0.6181 (tpp) cc_final: 0.5912 (tpp) REVERT: V 82 ARG cc_start: 0.3833 (mtm-85) cc_final: 0.3363 (mtm-85) REVERT: b 124 TYR cc_start: 0.7276 (t80) cc_final: 0.6936 (t80) REVERT: e 51 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (mtmt) REVERT: r 51 GLN cc_start: 0.6638 (mt0) cc_final: 0.6046 (mm-40) REVERT: w 646 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4144 (tm-30) REVERT: y 93 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6362 (ptpp) REVERT: y 162 HIS cc_start: 0.4555 (OUTLIER) cc_final: 0.3881 (m90) outliers start: 219 outliers final: 122 residues processed: 860 average time/residue: 0.9256 time to fit residues: 1362.2972 Evaluate side-chains 748 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 620 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 3 GLN Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 123 ILE Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 43 LYS Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 196 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 93 LYS Chi-restraints excluded: chain y residue 137 VAL Chi-restraints excluded: chain y residue 148 THR Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain T residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 661 optimal weight: 0.0020 chunk 451 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 591 optimal weight: 7.9990 chunk 327 optimal weight: 0.0170 chunk 678 optimal weight: 2.9990 chunk 549 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 405 optimal weight: 9.9990 chunk 713 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 overall best weight: 1.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 182 ASN A ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 HIS ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 HIS ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 102221 Z= 0.171 Angle : 0.575 15.485 149232 Z= 0.293 Chirality : 0.035 0.268 18627 Planarity : 0.004 0.075 10522 Dihedral : 22.998 179.128 41948 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 3.38 % Allowed : 21.55 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.04 (0.11), residues: 6010 helix: 0.83 (0.11), residues: 2366 sheet: -0.14 (0.18), residues: 840 loop : -0.67 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP w 16 HIS 0.007 0.001 HIS b 79 PHE 0.022 0.001 PHE b 53 TYR 0.021 0.001 TYR E 177 ARG 0.010 0.000 ARG r 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 698 time to evaluate : 5.591 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: 3 3 GLN cc_start: 0.4688 (OUTLIER) cc_final: 0.4356 (tm-30) REVERT: 8 39 MET cc_start: 0.2517 (ptp) cc_final: -0.0690 (ppp) REVERT: C 76 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6550 (mp) REVERT: C 174 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8173 (tt) REVERT: G 54 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6695 (mm-30) REVERT: G 57 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6927 (mmp-170) REVERT: G 84 LYS cc_start: 0.4931 (mttt) cc_final: 0.4102 (pttt) REVERT: G 162 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7558 (mt) REVERT: P 48 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6840 (mm) REVERT: P 75 GLU cc_start: 0.7534 (pt0) cc_final: 0.7282 (pt0) REVERT: S 46 MET cc_start: 0.8208 (ppp) cc_final: 0.7873 (ppp) REVERT: V 82 ARG cc_start: 0.3762 (mtm-85) cc_final: 0.3354 (mtm-85) REVERT: b 124 TYR cc_start: 0.7206 (t80) cc_final: 0.6895 (t80) REVERT: h 73 LYS cc_start: 0.7727 (tptm) cc_final: 0.7524 (tttp) REVERT: i 48 PHE cc_start: 0.6035 (m-80) cc_final: 0.5812 (m-80) REVERT: w 646 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4111 (tm-30) REVERT: y 93 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6498 (ptpp) REVERT: z 93 LYS cc_start: 0.7210 (ttmm) cc_final: 0.6528 (mmpt) REVERT: z 112 LYS cc_start: 0.6523 (tppt) cc_final: 0.5985 (mmtt) outliers start: 152 outliers final: 98 residues processed: 785 average time/residue: 0.9094 time to fit residues: 1220.4891 Evaluate side-chains 739 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 634 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 3 GLN Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 105 ILE Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain b residue 18 PHE Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 51 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 2 ARG Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain u residue 77 ASN Chi-restraints excluded: chain w residue 96 SER Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 93 LYS Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 137 VAL Chi-restraints excluded: chain y residue 148 THR Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 267 optimal weight: 7.9990 chunk 715 optimal weight: 2.9990 chunk 157 optimal weight: 40.0000 chunk 466 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 795 optimal weight: 30.0000 chunk 660 optimal weight: 3.9990 chunk 368 optimal weight: 0.0020 chunk 66 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 417 optimal weight: 0.7980 overall best weight: 2.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 HIS X 84 HIS ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 ASN b 79 HIS ** b 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 4 GLN g 3 GLN ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 84 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 HIS ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 102221 Z= 0.361 Angle : 0.708 24.749 149232 Z= 0.355 Chirality : 0.041 0.298 18627 Planarity : 0.006 0.076 10522 Dihedral : 23.032 179.274 41948 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 4.15 % Allowed : 21.88 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 (0.11), residues: 6010 helix: 0.64 (0.11), residues: 2364 sheet: -0.26 (0.18), residues: 850 loop : -0.74 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP w 16 HIS 0.023 0.002 HIS r 68 PHE 0.041 0.002 PHE y 222 TYR 0.030 0.002 TYR j 66 ARG 0.020 0.001 ARG r 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 660 time to evaluate : 5.674 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: 8 39 MET cc_start: 0.3159 (ptp) cc_final: -0.0349 (ppp) REVERT: C 76 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6819 (mp) REVERT: C 174 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8304 (tt) REVERT: F 249 MET cc_start: 0.7656 (mmt) cc_final: 0.7324 (mmt) REVERT: H 113 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6361 (mmm-85) REVERT: L 111 ARG cc_start: 0.7864 (tmm-80) cc_final: 0.7596 (ttp-170) REVERT: M 40 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: P 31 GLU cc_start: 0.5601 (mm-30) cc_final: 0.5394 (mm-30) REVERT: P 48 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7493 (mm) REVERT: P 154 GLU cc_start: 0.6551 (pt0) cc_final: 0.6339 (pt0) REVERT: Q 92 GLU cc_start: 0.8439 (pm20) cc_final: 0.8006 (pm20) REVERT: S 46 MET cc_start: 0.8155 (ppp) cc_final: 0.7949 (ppp) REVERT: V 111 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4831 (pmm) REVERT: b 7 LYS cc_start: 0.4941 (tmtt) cc_final: 0.4409 (tmtt) REVERT: b 124 TYR cc_start: 0.7256 (t80) cc_final: 0.7000 (t80) REVERT: e 51 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7970 (mtmt) REVERT: h 73 LYS cc_start: 0.7977 (tptm) cc_final: 0.7735 (tttp) REVERT: w 646 GLU cc_start: 0.5351 (OUTLIER) cc_final: 0.4382 (tm-30) REVERT: y 93 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6386 (ptpp) REVERT: z 93 LYS cc_start: 0.7160 (ttmm) cc_final: 0.6674 (mmpt) outliers start: 186 outliers final: 124 residues processed: 782 average time/residue: 0.9383 time to fit residues: 1258.9749 Evaluate side-chains 739 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 606 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 111 MET Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 111 THR Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 2 ARG Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 43 LYS Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain w residue 96 SER Chi-restraints excluded: chain w residue 102 GLN Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 139 LEU Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 196 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 93 LYS Chi-restraints excluded: chain y residue 148 THR Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 766 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 580 optimal weight: 40.0000 chunk 449 optimal weight: 6.9990 chunk 669 optimal weight: 0.9980 chunk 444 optimal weight: 5.9990 chunk 792 optimal weight: 7.9990 chunk 495 optimal weight: 9.9990 chunk 483 optimal weight: 7.9990 chunk 365 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 4 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 299 GLN L 146 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 HIS ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 13 ASN ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 102221 Z= 0.391 Angle : 0.709 17.799 149232 Z= 0.355 Chirality : 0.042 0.281 18627 Planarity : 0.006 0.073 10522 Dihedral : 23.097 179.703 41948 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 4.46 % Allowed : 22.05 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.33 (0.11), residues: 6010 helix: 0.58 (0.11), residues: 2362 sheet: -0.23 (0.18), residues: 824 loop : -0.83 (0.12), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP V 87 HIS 0.011 0.002 HIS B 198 PHE 0.060 0.002 PHE b 150 TYR 0.036 0.002 TYR r 6 ARG 0.025 0.001 ARG V 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 654 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: 8 39 MET cc_start: 0.3632 (ptp) cc_final: 0.3341 (ptm) REVERT: F 89 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7603 (mtmm) REVERT: F 249 MET cc_start: 0.7631 (mmt) cc_final: 0.7386 (mmt) REVERT: G 173 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6986 (mtp) REVERT: H 113 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6351 (mmm-85) REVERT: L 111 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7733 (ttp-170) REVERT: M 40 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6382 (m-30) REVERT: P 48 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7733 (mm) REVERT: Q 92 GLU cc_start: 0.8504 (pm20) cc_final: 0.8283 (pm20) REVERT: S 120 ILE cc_start: 0.7758 (mm) cc_final: 0.7552 (mm) REVERT: X 98 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8918 (p) REVERT: Y 83 ARG cc_start: 0.6817 (ptp-110) cc_final: 0.6602 (mtm110) REVERT: f 102 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7087 (mpp) REVERT: h 73 LYS cc_start: 0.8238 (tptm) cc_final: 0.8019 (tttp) REVERT: i 41 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8371 (tt) REVERT: w 646 GLU cc_start: 0.5215 (OUTLIER) cc_final: 0.4124 (tm-30) REVERT: z 93 LYS cc_start: 0.7113 (ttmm) cc_final: 0.6505 (mmpt) REVERT: z 112 LYS cc_start: 0.6027 (mmtm) cc_final: 0.5559 (mmtt) outliers start: 200 outliers final: 142 residues processed: 786 average time/residue: 0.9277 time to fit residues: 1248.1421 Evaluate side-chains 771 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 620 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 PHE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 8 residue 9 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 193 ASN Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain X residue 111 THR Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 76 LYS Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain k residue 67 VAL Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 49 LEU Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain w residue 96 SER Chi-restraints excluded: chain w residue 102 GLN Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 139 LEU Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 137 VAL Chi-restraints excluded: chain y residue 148 THR Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 490 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 chunk 473 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 503 optimal weight: 0.9990 chunk 539 optimal weight: 1.9990 chunk 391 optimal weight: 0.5980 chunk 73 optimal weight: 50.0000 chunk 622 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 96 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 ASN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN S 153 HIS a 139 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 102221 Z= 0.163 Angle : 0.586 19.678 149232 Z= 0.297 Chirality : 0.035 0.280 18627 Planarity : 0.004 0.064 10522 Dihedral : 23.003 179.801 41948 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 3.27 % Allowed : 24.29 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 6010 helix: 0.83 (0.11), residues: 2369 sheet: -0.24 (0.18), residues: 850 loop : -0.69 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 194 HIS 0.009 0.001 HIS R 58 PHE 0.055 0.002 PHE y 34 TYR 0.035 0.001 TYR r 6 ARG 0.012 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 658 time to evaluate : 5.571 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: 8 39 MET cc_start: 0.3483 (ptp) cc_final: 0.0049 (ppp) REVERT: B 211 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: F 249 MET cc_start: 0.7370 (mmt) cc_final: 0.7150 (mmt) REVERT: G 106 LYS cc_start: 0.8702 (tptp) cc_final: 0.8393 (tppt) REVERT: H 113 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6352 (mmm-85) REVERT: L 111 ARG cc_start: 0.7859 (tmm-80) cc_final: 0.7506 (ttp-170) REVERT: P 48 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7659 (mm) REVERT: Q 92 GLU cc_start: 0.8457 (pm20) cc_final: 0.8183 (pm20) REVERT: X 98 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8806 (p) REVERT: e 31 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8094 (tptm) REVERT: h 18 GLU cc_start: 0.7833 (pp20) cc_final: 0.7383 (pp20) REVERT: h 73 LYS cc_start: 0.8180 (tptm) cc_final: 0.7968 (tttp) REVERT: i 56 MET cc_start: 0.5295 (ppp) cc_final: 0.4726 (ppp) REVERT: w 646 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4419 (tm-30) REVERT: z 93 LYS cc_start: 0.7338 (ttmm) cc_final: 0.6934 (mmpt) outliers start: 146 outliers final: 102 residues processed: 742 average time/residue: 0.9011 time to fit residues: 1144.8276 Evaluate side-chains 734 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 626 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain e residue 31 LYS Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain k residue 67 VAL Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain w residue 102 GLN Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 196 VAL Chi-restraints excluded: chain w residue 475 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 148 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 720 optimal weight: 3.9990 chunk 759 optimal weight: 0.9990 chunk 692 optimal weight: 3.9990 chunk 738 optimal weight: 9.9990 chunk 758 optimal weight: 50.0000 chunk 444 optimal weight: 0.9990 chunk 321 optimal weight: 9.9990 chunk 579 optimal weight: 50.0000 chunk 226 optimal weight: 4.9990 chunk 667 optimal weight: 0.9980 chunk 698 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN S 153 HIS ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 139 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 102221 Z= 0.223 Angle : 0.602 16.417 149232 Z= 0.304 Chirality : 0.036 0.277 18627 Planarity : 0.004 0.065 10522 Dihedral : 22.942 179.895 41948 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 3.21 % Allowed : 24.29 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.03 (0.11), residues: 6010 helix: 0.88 (0.11), residues: 2360 sheet: -0.22 (0.18), residues: 841 loop : -0.66 (0.12), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 194 HIS 0.006 0.001 HIS N 192 PHE 0.038 0.002 PHE y 7 TYR 0.034 0.002 TYR r 6 ARG 0.014 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 640 time to evaluate : 5.516 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: 8 39 MET cc_start: 0.3474 (ptp) cc_final: 0.3072 (ptm) REVERT: G 106 LYS cc_start: 0.8732 (tptp) cc_final: 0.8390 (tppt) REVERT: H 94 TYR cc_start: 0.6618 (p90) cc_final: 0.6265 (p90) REVERT: H 113 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6443 (mmm-85) REVERT: H 135 SER cc_start: 0.7211 (t) cc_final: 0.6549 (t) REVERT: L 111 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7553 (ttp-170) REVERT: P 48 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7811 (mm) REVERT: Q 92 GLU cc_start: 0.8489 (pm20) cc_final: 0.8168 (pm20) REVERT: X 98 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8761 (p) REVERT: b 7 LYS cc_start: 0.5039 (tmtt) cc_final: 0.4547 (tmtt) REVERT: b 124 TYR cc_start: 0.7437 (t80) cc_final: 0.7173 (t80) REVERT: e 31 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8060 (tptm) REVERT: f 102 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6938 (mpp) REVERT: h 73 LYS cc_start: 0.8202 (tptm) cc_final: 0.7981 (tttp) REVERT: i 56 MET cc_start: 0.5004 (ppp) cc_final: 0.4648 (ppp) REVERT: w 646 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4543 (tm-30) REVERT: w 779 TYR cc_start: 0.2683 (p90) cc_final: 0.2399 (p90) REVERT: z 93 LYS cc_start: 0.7117 (ttmm) cc_final: 0.6638 (mmpt) outliers start: 143 outliers final: 112 residues processed: 719 average time/residue: 0.9008 time to fit residues: 1107.6176 Evaluate side-chains 734 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 616 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 31 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 76 LYS Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain k residue 67 VAL Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain w residue 102 GLN Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 128 LEU Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 196 VAL Chi-restraints excluded: chain w residue 475 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain w residue 760 VAL Chi-restraints excluded: chain w residue 786 MET Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 137 VAL Chi-restraints excluded: chain y residue 138 PHE Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain z residue 112 LYS Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 735 optimal weight: 40.0000 chunk 484 optimal weight: 10.0000 chunk 780 optimal weight: 20.0000 chunk 476 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 542 optimal weight: 20.0000 chunk 818 optimal weight: 20.0000 chunk 753 optimal weight: 20.0000 chunk 652 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 503 optimal weight: 1.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN O 43 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 HIS ** a 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 HIS ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 84 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.133 102221 Z= 0.727 Angle : 0.989 16.754 149232 Z= 0.481 Chirality : 0.054 0.358 18627 Planarity : 0.008 0.178 10522 Dihedral : 23.301 179.910 41948 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 3.38 % Allowed : 24.53 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.75 (0.11), residues: 6010 helix: 0.25 (0.11), residues: 2354 sheet: -0.46 (0.18), residues: 828 loop : -1.09 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP G 233 HIS 0.015 0.003 HIS N 192 PHE 0.064 0.003 PHE y 222 TYR 0.036 0.003 TYR r 6 ARG 0.027 0.001 ARG h 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12020 Ramachandran restraints generated. 6010 Oldfield, 0 Emsley, 6010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 627 time to evaluate : 5.558 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: 8 39 MET cc_start: 0.3852 (ptp) cc_final: 0.3550 (ptm) REVERT: B 34 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6821 (ptpp) REVERT: B 211 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: F 89 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7516 (mtmm) REVERT: G 173 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: H 94 TYR cc_start: 0.6716 (p90) cc_final: 0.6361 (p90) REVERT: H 113 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6417 (mmm-85) REVERT: L 111 ARG cc_start: 0.8179 (tmm-80) cc_final: 0.7809 (ttp-170) REVERT: N 159 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8496 (mtp180) REVERT: V 3 ARG cc_start: 0.1322 (ptt90) cc_final: 0.0977 (ptt180) REVERT: b 7 LYS cc_start: 0.5126 (tmtt) cc_final: 0.4777 (tmtt) REVERT: b 124 TYR cc_start: 0.7347 (t80) cc_final: 0.7073 (t80) REVERT: b 432 MET cc_start: 0.7939 (tmm) cc_final: 0.7426 (tmm) REVERT: e 31 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8207 (tptm) REVERT: f 102 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6933 (mpp) REVERT: h 73 LYS cc_start: 0.8429 (tptm) cc_final: 0.8195 (tttp) REVERT: i 59 ILE cc_start: 0.6558 (mm) cc_final: 0.6346 (mm) REVERT: r 52 GLU cc_start: 0.7261 (pp20) cc_final: 0.6977 (pp20) REVERT: u 43 LYS cc_start: 0.3109 (OUTLIER) cc_final: 0.2698 (tptp) REVERT: w 646 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.4655 (tm-30) REVERT: z 93 LYS cc_start: 0.7165 (ttmm) cc_final: 0.6628 (mmpt) outliers start: 151 outliers final: 118 residues processed: 720 average time/residue: 0.9139 time to fit residues: 1128.8227 Evaluate side-chains 732 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 604 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 32 TYR Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 8 residue 9 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 34 HIS Chi-restraints excluded: chain M residue 60 HIS Chi-restraints excluded: chain M residue 109 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 159 ARG Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 116 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain X residue 111 THR Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 429 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain e residue 31 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 76 LYS Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 48 VAL Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 42 MET Chi-restraints excluded: chain u residue 43 LYS Chi-restraints excluded: chain u residue 55 TYR Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain w residue 96 SER Chi-restraints excluded: chain w residue 102 GLN Chi-restraints excluded: chain w residue 118 ASP Chi-restraints excluded: chain w residue 128 LEU Chi-restraints excluded: chain w residue 190 VAL Chi-restraints excluded: chain w residue 196 VAL Chi-restraints excluded: chain w residue 475 VAL Chi-restraints excluded: chain w residue 646 GLU Chi-restraints excluded: chain w residue 758 LEU Chi-restraints excluded: chain w residue 759 VAL Chi-restraints excluded: chain y residue 95 GLN Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 137 VAL Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain y residue 209 ASP Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 399 optimal weight: 0.9980 chunk 517 optimal weight: 50.0000 chunk 694 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 601 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 653 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 670 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 HIS ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 HIS d 50 GLN ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 HIS ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.173281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.156708 restraints weight = 244112.339| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 0.80 r_work: 0.4005 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 102221 Z= 0.278 Angle : 0.670 18.462 149232 Z= 0.338 Chirality : 0.039 0.294 18627 Planarity : 0.005 0.071 10522 Dihedral : 23.167 179.640 41948 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 25.15 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.42 (0.11), residues: 6010 helix: 0.58 (0.11), residues: 2354 sheet: -0.42 (0.18), residues: 848 loop : -0.92 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP u 51 HIS 0.007 0.001 HIS F 86 PHE 0.037 0.002 PHE g 62 TYR 0.036 0.002 TYR r 6 ARG 0.014 0.001 ARG C 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22903.80 seconds wall clock time: 405 minutes 21.22 seconds (24321.22 seconds total)