Starting phenix.real_space_refine on Mon Mar 18 06:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swa_10321/03_2024/6swa_10321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swa_10321/03_2024/6swa_10321.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/6swa_10321/03_2024/6swa_10321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swa_10321/03_2024/6swa_10321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swa_10321/03_2024/6swa_10321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swa_10321/03_2024/6swa_10321.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= 0.908 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3888 5.49 5 Mg 247 5.21 5 S 250 5.16 5 C 71603 2.51 5 N 25901 2.21 5 O 36268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K GLU 142": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L ARG 119": "NH1" <-> "NH2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M ARG 20": "NH1" <-> "NH2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M GLU 160": "OE1" <-> "OE2" Residue "M ARG 169": "NH1" <-> "NH2" Residue "M ARG 193": "NH1" <-> "NH2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 158": "OE1" <-> "OE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N GLU 182": "OE1" <-> "OE2" Residue "N GLU 186": "OE1" <-> "OE2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O GLU 99": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P GLU 129": "OE1" <-> "OE2" Residue "Q GLU 9": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "R GLU 118": "OE1" <-> "OE2" Residue "R GLU 147": "OE1" <-> "OE2" Residue "R GLU 157": "OE1" <-> "OE2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S ARG 65": "NH1" <-> "NH2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "V ARG 67": "NH1" <-> "NH2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 91": "OE1" <-> "OE2" Residue "V GLU 133": "OE1" <-> "OE2" Residue "W GLU 88": "OE1" <-> "OE2" Residue "W GLU 120": "OE1" <-> "OE2" Residue "X GLU 120": "OE1" <-> "OE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z ARG 41": "NH1" <-> "NH2" Residue "a ARG 17": "NH1" <-> "NH2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b GLU 94": "OE1" <-> "OE2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "e ARG 76": "NH1" <-> "NH2" Residue "f ARG 7": "NH1" <-> "NH2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 51": "NH1" <-> "NH2" Residue "f GLU 67": "OE1" <-> "OE2" Residue "f GLU 100": "OE1" <-> "OE2" Residue "f ARG 109": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "g ARG 4": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g GLU 59": "OE1" <-> "OE2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 46": "NH1" <-> "NH2" Residue "k GLU 79": "OE1" <-> "OE2" Residue "k ARG 83": "NH1" <-> "NH2" Residue "m ARG 9": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "o ARG 108": "NH1" <-> "NH2" Residue "o ARG 136": "NH1" <-> "NH2" Residue "o ARG 151": "NH1" <-> "NH2" Residue "o GLU 168": "OE1" <-> "OE2" Residue "o ARG 172": "NH1" <-> "NH2" Residue "o ARG 173": "NH1" <-> "NH2" Residue "o GLU 175": "OE1" <-> "OE2" Residue "p ARG 98": "NH1" <-> "NH2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t GLU 50": "OE1" <-> "OE2" Residue "t GLU 58": "OE1" <-> "OE2" Residue "t GLU 69": "OE1" <-> "OE2" Residue "t ARG 138": "NH1" <-> "NH2" Residue "t GLU 198": "OE1" <-> "OE2" Residue "t GLU 219": "OE1" <-> "OE2" Residue "t PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 290": "NH1" <-> "NH2" Residue "t GLU 353": "OE1" <-> "OE2" 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: 138160 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1930 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3178 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2897 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "D" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2395 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain: "E" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1947 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain: "G" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1879 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 14, 'TRANS': 219} Chain: "H" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1527 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 3, 'TRANS': 187} Chain: "I" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1692 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "K" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1660 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "L" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "M" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "N" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1599 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "O" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "P" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1504 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1447 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "R" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain: "S" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 826 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "T" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "U" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 520 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "V" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 966 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "W" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1064 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "X" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1103 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Y" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1164 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 558 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "a" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "c" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1064 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "d" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "e" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "f" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "g" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "h" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "i" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 568 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "j" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 443 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "m" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "n" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "o" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "p" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "q" Number of atoms: 77430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3612, 77430 Classifications: {'RNA': 3612} Modifications used: {'rna2p_pur': 345, 'rna2p_pyr': 222, 'rna3p_pur': 1631, 'rna3p_pyr': 1414} Link IDs: {'rna2p': 567, 'rna3p': 3044} Chain breaks: 11 Chain: "r" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3337 Classifications: {'RNA': 157} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 61, 'rna3p_pyr': 68} Link IDs: {'rna2p': 28, 'rna3p': 128} Chain: "s" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2541 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 11, 'rna3p': 107} Chain: "t" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2739 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 340} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Unusual residues: {' MG': 223} Classifications: {'undetermined': 223} Link IDs: {None: 222} Chain: "r" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45559 SG CYS h 19 111.732 145.542 102.609 1.00 76.77 S ATOM 45587 SG CYS h 22 107.986 146.097 105.915 1.00 80.70 S ATOM 45678 SG CYS h 34 111.551 142.635 104.709 1.00 72.83 S ATOM 45697 SG CYS h 37 108.351 143.565 103.394 1.00 74.87 S ATOM 47861 SG CYS m 12 61.501 71.952 136.929 1.00 99.43 S ATOM 48354 SG CYS m 72 61.755 68.159 134.274 1.00103.06 S ATOM 48391 SG CYS m 77 59.686 71.206 133.511 1.00107.35 S ATOM 48933 SG CYS n 39 150.566 109.131 61.758 1.00 84.43 S ATOM 48956 SG CYS n 42 151.577 112.048 59.922 1.00 85.96 S Time building chain proxies: 51.56, per 1000 atoms: 0.37 Number of scatterers: 138160 At special positions: 0 Unit cell: (237.479, 244.113, 270.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 250 16.00 P 3888 15.00 Mg 247 11.99 O 36268 8.00 N 25901 7.00 C 71603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS O 57 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS k 96 " - pdb=" SG CYS k 99 " distance=1.67 Simple disulfide: pdb=" SG CYS k 99 " - pdb=" SG CYS k 110 " distance=2.92 Simple disulfide: pdb=" SG CYS k 99 " - pdb=" SG CYS k 115 " distance=2.73 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: 53.01 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN h 101 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 37 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 34 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 19 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 22 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 12 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 77 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 72 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 42 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 39 " Number of angles added : 6 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12576 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 66 sheets defined 37.2% alpha, 13.9% beta 967 base pairs and 1996 stacking pairs defined. Time for finding SS restraints: 42.49 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 removed outlier: 3.793A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 12 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 13 " --> pdb=" O LYS A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 13' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 173 through 177 removed outlier: 4.087A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.773A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (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 134 through 139 removed outlier: 3.818A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.728A pdb=" N ASP B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.970A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.643A pdb=" N PHE C 28 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 46 removed outlier: 3.955A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.799A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.681A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.554A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.650A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 331 through 360 removed outlier: 3.514A pdb=" N LEU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.654A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.857A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 37 removed outlier: 3.708A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.693A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.626A pdb=" N TYR D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 297 removed outlier: 3.663A pdb=" N PHE D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.529A pdb=" N HIS E 136 " --> pdb=" O PHE E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.677A pdb=" N LEU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) Proline residue: E 259 - end of helix Processing helix chain 'E' and resid 266 through 273 removed outlier: 3.655A pdb=" N TYR E 270 " --> pdb=" O GLN E 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 77 removed outlier: 3.514A pdb=" N ARG F 23 " --> pdb=" O LYS F 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU F 68 " --> pdb=" O MET F 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 69 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.983A pdb=" N VAL F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 136 removed outlier: 3.595A pdb=" N ASN F 131 " --> pdb=" O LYS F 127 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 156 Processing helix chain 'F' and resid 171 through 180 removed outlier: 4.047A pdb=" N ILE F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 196 Processing helix chain 'F' and resid 200 through 208 removed outlier: 3.905A pdb=" N ALA F 204 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.721A pdb=" N LEU F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.642A pdb=" N ARG G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 100 Processing helix chain 'G' and resid 106 through 125 removed outlier: 3.718A pdb=" N ALA G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 removed outlier: 3.627A pdb=" N ASN G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 4.606A pdb=" N PHE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 194 removed outlier: 4.463A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 224 removed outlier: 3.593A pdb=" N LEU G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU G 220 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 262 removed outlier: 3.926A pdb=" N ARG G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 250 " --> pdb=" O SER G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.597A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.727A pdb=" N ASN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 removed outlier: 3.955A pdb=" N ARG I 10 " --> pdb=" O ARG I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 80 removed outlier: 3.690A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 159 removed outlier: 3.682A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 187 removed outlier: 3.733A pdb=" N ALA I 186 " --> pdb=" O GLU I 182 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU I 187 " --> pdb=" O ASP I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.961A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 removed outlier: 3.826A pdb=" N LEU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J 42 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 removed outlier: 3.605A pdb=" N VAL J 89 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 111 through 116 removed outlier: 3.594A pdb=" N ASP J 114 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY J 116 " --> pdb=" O ILE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 142 removed outlier: 3.940A pdb=" N ILE J 141 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA J 142 " --> pdb=" O PHE J 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 142' Processing helix chain 'J' and resid 158 through 171 removed outlier: 3.956A pdb=" N ALA J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 46 Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'K' and resid 87 through 95 removed outlier: 3.644A pdb=" N ALA K 91 " --> pdb=" O HIS K 87 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 124 removed outlier: 3.618A pdb=" N ALA K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'K' and resid 171 through 176 removed outlier: 3.918A pdb=" N LYS K 174 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE K 176 " --> pdb=" O GLU K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 191 removed outlier: 3.600A pdb=" N LEU K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 206 Processing helix chain 'L' and resid 69 through 81 removed outlier: 3.865A pdb=" N LYS L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 88 removed outlier: 3.874A pdb=" N LYS L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA L 87 " --> pdb=" O ASN L 83 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 88 " --> pdb=" O THR L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 104 removed outlier: 3.505A pdb=" N LYS L 94 " --> pdb=" O ARG L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 139 removed outlier: 3.598A pdb=" N LYS L 117 " --> pdb=" O MET L 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET L 118 " --> pdb=" O LYS L 114 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 132 " --> pdb=" O LYS L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 4.082A pdb=" N LYS M 13 " --> pdb=" O GLU M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 33 removed outlier: 3.788A pdb=" N LEU M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN M 32 " --> pdb=" O TRP M 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 33 " --> pdb=" O GLN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 50 Processing helix chain 'M' and resid 75 through 79 removed outlier: 3.652A pdb=" N GLY M 78 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 97 through 110 Processing helix chain 'M' and resid 139 through 144 Processing helix chain 'M' and resid 145 through 152 removed outlier: 3.639A pdb=" N GLN M 149 " --> pdb=" O PRO M 146 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP M 150 " --> pdb=" O ASP M 147 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE M 151 " --> pdb=" O THR M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 165 through 173 removed outlier: 3.744A pdb=" N LYS M 170 " --> pdb=" O SER M 166 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 181 removed outlier: 4.094A pdb=" N HIS M 181 " --> pdb=" O HIS M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 196 Processing helix chain 'N' and resid 15 through 28 removed outlier: 3.883A pdb=" N ILE N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 40 removed outlier: 3.619A pdb=" N GLY N 40 " --> pdb=" O ARG N 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 37 through 40' Processing helix chain 'N' and resid 46 through 60 removed outlier: 3.677A pdb=" N LYS N 60 " --> pdb=" O ALA N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 88 removed outlier: 3.650A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 99 Processing helix chain 'N' and resid 109 through 114 removed outlier: 4.507A pdb=" N LYS N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 123 Processing helix chain 'N' and resid 124 through 129 Processing helix chain 'N' and resid 138 through 144 Processing helix chain 'N' and resid 149 through 185 removed outlier: 3.641A pdb=" N MET N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 197 removed outlier: 3.564A pdb=" N VAL N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 12 No H-bonds generated for 'chain 'O' and resid 10 through 12' Processing helix chain 'O' and resid 25 through 37 Processing helix chain 'O' and resid 40 through 53 Processing helix chain 'O' and resid 71 through 77 removed outlier: 3.787A pdb=" N LYS O 74 " --> pdb=" O ALA O 71 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN O 75 " --> pdb=" O GLN O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 106 Processing helix chain 'P' and resid 22 through 39 removed outlier: 3.641A pdb=" N PHE P 34 " --> pdb=" O LYS P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 53 removed outlier: 3.730A pdb=" N PHE P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 72 removed outlier: 3.703A pdb=" N MET P 66 " --> pdb=" O SER P 62 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 115 removed outlier: 3.586A pdb=" N SER P 111 " --> pdb=" O SER P 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG P 112 " --> pdb=" O ARG P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 130 Processing helix chain 'P' and resid 146 through 151 Processing helix chain 'Q' and resid 36 through 52 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'Q' and resid 120 through 124 removed outlier: 3.802A pdb=" N ILE Q 124 " --> pdb=" O ALA Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 144 Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.613A pdb=" N THR R 29 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 58 removed outlier: 3.743A pdb=" N HIS R 58 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 123 removed outlier: 3.789A pdb=" N ASP R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU R 121 " --> pdb=" O LYS R 117 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 32 removed outlier: 3.813A pdb=" N VAL S 29 " --> pdb=" O CYS S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 47 removed outlier: 3.799A pdb=" N PHE S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 94 removed outlier: 3.951A pdb=" N LEU S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 129 Processing helix chain 'T' and resid 129 through 136 removed outlier: 3.907A pdb=" N ASN T 135 " --> pdb=" O ARG T 131 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA T 136 " --> pdb=" O ILE T 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 42 Processing helix chain 'U' and resid 52 through 60 removed outlier: 3.623A pdb=" N ARG U 56 " --> pdb=" O THR U 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 76 Processing helix chain 'V' and resid 83 through 92 removed outlier: 3.580A pdb=" N LYS V 89 " --> pdb=" O SER V 85 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU V 91 " --> pdb=" O MET V 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP V 92 " --> pdb=" O LYS V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 145 through 153 removed outlier: 3.599A pdb=" N VAL V 149 " --> pdb=" O ASP V 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 20 Processing helix chain 'W' and resid 22 through 30 removed outlier: 4.249A pdb=" N LYS W 28 " --> pdb=" O HIS W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 43 removed outlier: 3.505A pdb=" N GLN W 40 " --> pdb=" O LYS W 36 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 102 No H-bonds generated for 'chain 'W' and resid 100 through 102' Processing helix chain 'W' and resid 112 through 127 removed outlier: 3.537A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 66 removed outlier: 3.680A pdb=" N LYS X 64 " --> pdb=" O LYS X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 102 removed outlier: 4.097A pdb=" N PHE X 101 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG X 102 " --> pdb=" O ASP X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 124 removed outlier: 3.781A pdb=" N ARG X 121 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR X 124 " --> pdb=" O GLU X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 132 removed outlier: 3.876A pdb=" N PHE X 131 " --> pdb=" O ASN X 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 49 Processing helix chain 'Y' and resid 83 through 93 removed outlier: 4.185A pdb=" N ARG Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN Y 93 " --> pdb=" O ASN Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 107 Processing helix chain 'Y' and resid 130 through 139 Processing helix chain 'Z' and resid 12 through 20 removed outlier: 3.978A pdb=" N ASN Z 19 " --> pdb=" O LYS Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 49 Processing helix chain 'Z' and resid 49 through 69 removed outlier: 4.324A pdb=" N GLY Z 53 " --> pdb=" O HIS Z 49 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS Z 55 " --> pdb=" O LYS Z 51 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Z 59 " --> pdb=" O LYS Z 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 14 through 24 removed outlier: 3.862A pdb=" N LEU a 20 " --> pdb=" O SER a 16 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS a 23 " --> pdb=" O GLN a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 40 removed outlier: 3.581A pdb=" N THR a 34 " --> pdb=" O GLY a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 Processing helix chain 'a' and resid 77 through 86 Processing helix chain 'b' and resid 29 through 33 Processing helix chain 'b' and resid 37 through 40 Processing helix chain 'b' and resid 41 through 57 Processing helix chain 'b' and resid 65 through 73 Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 43 through 48 removed outlier: 3.712A pdb=" N ARG c 47 " --> pdb=" O ASN c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 61 Processing helix chain 'c' and resid 85 through 90 removed outlier: 4.322A pdb=" N MET c 90 " --> pdb=" O VAL c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 119 removed outlier: 3.577A pdb=" N LYS c 109 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA c 110 " --> pdb=" O LYS c 106 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 42 removed outlier: 3.641A pdb=" N THR d 39 " --> pdb=" O ARG d 36 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU d 40 " --> pdb=" O ASP d 37 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE d 41 " --> pdb=" O GLU d 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 97 removed outlier: 3.586A pdb=" N ILE d 97 " --> pdb=" O ALA d 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 66 removed outlier: 3.791A pdb=" N MET e 65 " --> pdb=" O LYS e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 72 Processing helix chain 'e' and resid 83 through 113 removed outlier: 3.544A pdb=" N VAL e 87 " --> pdb=" O CYS e 83 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG e 88 " --> pdb=" O ALA e 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 10 removed outlier: 3.659A pdb=" N LEU f 9 " --> pdb=" O LYS f 5 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG f 10 " --> pdb=" O ALA f 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 5 through 10' Processing helix chain 'f' and resid 13 through 37 removed outlier: 3.698A pdb=" N LYS f 19 " --> pdb=" O GLU f 15 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP f 23 " --> pdb=" O LYS f 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU f 24 " --> pdb=" O GLN f 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL f 36 " --> pdb=" O ARG f 32 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR f 37 " --> pdb=" O VAL f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 45 through 74 removed outlier: 4.329A pdb=" N VAL f 49 " --> pdb=" O SER f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 93 removed outlier: 3.641A pdb=" N ARG f 92 " --> pdb=" O THR f 88 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG f 93 " --> pdb=" O ARG f 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 88 through 93' Processing helix chain 'f' and resid 96 through 102 Processing helix chain 'f' and resid 104 through 114 Processing helix chain 'g' and resid 34 through 49 Processing helix chain 'g' and resid 51 through 63 Processing helix chain 'g' and resid 66 through 77 Processing helix chain 'g' and resid 79 through 97 removed outlier: 4.186A pdb=" N MET g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 removed outlier: 3.562A pdb=" N GLY h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 50 through 56 removed outlier: 4.300A pdb=" N LYS h 54 " --> pdb=" O SER h 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG h 55 " --> pdb=" O ALA h 51 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG h 56 " --> pdb=" O LYS h 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 50 through 56' Processing helix chain 'h' and resid 66 through 75 removed outlier: 3.619A pdb=" N VAL h 70 " --> pdb=" O HIS h 66 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR h 71 " --> pdb=" O LEU h 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG h 72 " --> pdb=" O LYS h 68 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG h 75 " --> pdb=" O TYR h 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 16 removed outlier: 3.788A pdb=" N LEU i 13 " --> pdb=" O LYS i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 55 removed outlier: 3.558A pdb=" N LYS i 55 " --> pdb=" O GLU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 60 removed outlier: 3.620A pdb=" N LEU i 60 " --> pdb=" O LYS i 57 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 20 removed outlier: 3.576A pdb=" N LYS j 16 " --> pdb=" O PHE j 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 91 removed outlier: 3.629A pdb=" N GLN k 84 " --> pdb=" O PRO k 80 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR k 89 " --> pdb=" O LEU k 85 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.901A pdb=" N SER l 24 " --> pdb=" O MET l 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 46 Processing helix chain 'n' and resid 9 through 14 removed outlier: 3.577A pdb=" N LYS n 13 " --> pdb=" O ILE n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 20 through 35 removed outlier: 4.011A pdb=" N LYS n 28 " --> pdb=" O LYS n 24 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE n 29 " --> pdb=" O MET n 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS n 34 " --> pdb=" O GLU n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 89 removed outlier: 3.560A pdb=" N THR n 78 " --> pdb=" O THR n 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.519A pdb=" N SER o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 18 through 20 No H-bonds generated for 'chain 'o' and resid 18 through 20' Processing helix chain 'o' and resid 28 through 34 removed outlier: 3.700A pdb=" N ASN o 34 " --> pdb=" O ASN o 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 48 Processing helix chain 'o' and resid 60 through 73 Processing helix chain 'o' and resid 77 through 81 Processing helix chain 'o' and resid 84 through 89 Processing helix chain 'o' and resid 90 through 112 Processing helix chain 'o' and resid 116 through 129 removed outlier: 3.735A pdb=" N SER o 122 " --> pdb=" O HIS o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 134 through 185 removed outlier: 3.631A pdb=" N ARG o 176 " --> pdb=" O ARG o 172 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU o 177 " --> pdb=" O ARG o 173 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE o 184 " --> pdb=" O LYS o 180 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE o 185 " --> pdb=" O LYS o 181 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 11 removed outlier: 3.750A pdb=" N VAL p 9 " --> pdb=" O LEU p 5 " (cutoff:3.500A) Processing helix chain 'p' and resid 87 through 99 Processing helix chain 'p' and resid 106 through 122 Processing helix chain 't' and resid 14 through 37 removed outlier: 4.016A pdb=" N VAL t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 59 removed outlier: 4.133A pdb=" N LEU t 48 " --> pdb=" O SER t 44 " (cutoff:3.500A) Processing helix chain 't' and resid 136 through 157 removed outlier: 3.912A pdb=" N CYS t 149 " --> pdb=" O ALA t 145 " (cutoff:3.500A) Processing helix chain 't' and resid 163 through 177 removed outlier: 3.811A pdb=" N TRP t 170 " --> pdb=" O VAL t 166 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN t 171 " --> pdb=" O THR t 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS t 172 " --> pdb=" O GLU t 168 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL t 173 " --> pdb=" O ALA t 169 " (cutoff:3.500A) Processing helix chain 't' and resid 206 through 213 removed outlier: 3.845A pdb=" N LYS t 210 " --> pdb=" O THR t 206 " (cutoff:3.500A) Processing helix chain 't' and resid 259 through 273 Processing helix chain 't' and resid 279 through 283 removed outlier: 3.688A pdb=" N PHE t 283 " --> pdb=" O LEU t 280 " (cutoff:3.500A) Processing helix chain 't' and resid 285 through 292 Processing helix chain 't' and resid 293 through 299 removed outlier: 3.568A pdb=" N HIS t 299 " --> pdb=" O GLU t 295 " (cutoff:3.500A) Processing helix chain 't' and resid 351 through 359 removed outlier: 3.702A pdb=" N GLN t 359 " --> pdb=" O LYS t 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.374A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A 64 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.042A pdb=" N ILE A 82 " --> pdb=" O ALA n 65 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE n 54 " --> pdb=" O ARG n 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.569A pdb=" N LEU A 102 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 163 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 116 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 53 removed outlier: 5.530A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 52 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 330 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 287 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET B 332 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS B 283 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN B 281 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 217 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.841A pdb=" N VAL B 57 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 59 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP B 364 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 105 removed outlier: 4.911A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 93 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 89 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 161 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 91 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 159 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 4.911A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 93 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 229 Processing sheet with id=AA9, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.643A pdb=" N VAL C 10 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.602A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 152 through 154 removed outlier: 5.954A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 253 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 230 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 78 removed outlier: 5.389A pdb=" N ILE D 74 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR D 66 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS D 76 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.931A pdb=" N GLY E 97 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG E 105 " --> pdb=" O GLY E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 187 through 189 removed outlier: 7.329A pdb=" N LEU E 174 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 160 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR E 148 " --> pdb=" O PHE E 164 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL E 149 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 140 through 143 removed outlier: 4.337A pdb=" N ASN F 119 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'G' and resid 137 through 138 removed outlier: 6.415A pdb=" N VAL G 155 " --> pdb=" O CYS G 182 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 157 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 10 removed outlier: 7.331A pdb=" N ILE H 4 " --> pdb=" O TRP H 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AC2, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.925A pdb=" N ARG H 89 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS H 184 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 102 through 105 Processing sheet with id=AC4, first strand: chain 'I' and resid 86 through 89 removed outlier: 4.100A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 138 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU I 48 " --> pdb=" O THR I 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 58 through 61 removed outlier: 7.002A pdb=" N ILE I 97 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR I 125 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS I 95 " --> pdb=" O THR I 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AC7, first strand: chain 'J' and resid 49 through 52 removed outlier: 7.467A pdb=" N VAL J 133 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU J 20 " --> pdb=" O TYR J 131 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR J 131 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 93 through 95 Processing sheet with id=AC9, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.330A pdb=" N ASP K 23 " --> pdb=" O LEU M 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AD2, first strand: chain 'K' and resid 125 through 127 removed outlier: 4.232A pdb=" N LYS f 118 " --> pdb=" O PHE K 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 166 through 168 removed outlier: 3.695A pdb=" N ARG K 167 " --> pdb=" O ALA Y 98 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE Y 123 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS Y 125 " --> pdb=" O PRO Y 99 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE Y 101 " --> pdb=" O LYS Y 125 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL Y 124 " --> pdb=" O VAL Y 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 48 through 51 removed outlier: 7.755A pdb=" N ARG L 35 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL L 30 " --> pdb=" O ARG L 35 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU L 37 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG L 11 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL L 12 " --> pdb=" O THR L 58 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 36 through 39 removed outlier: 4.160A pdb=" N ILE M 61 " --> pdb=" O ALA M 39 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY M 122 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU M 131 " --> pdb=" O TRP M 120 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP M 120 " --> pdb=" O GLU M 131 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE M 133 " --> pdb=" O SER M 118 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N SER M 118 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE M 135 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU M 116 " --> pdb=" O ILE M 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 6 through 10 removed outlier: 6.182A pdb=" N LEU N 7 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL N 36 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU N 9 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL N 33 " --> pdb=" O LYS N 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AD8, first strand: chain 'O' and resid 14 through 22 removed outlier: 4.008A pdb=" N ASN O 21 " --> pdb=" O CYS O 144 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS O 144 " --> pdb=" O ASN O 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS O 116 " --> pdb=" O ILE O 149 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR O 151 " --> pdb=" O ILE O 114 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE O 114 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 58 through 59 Processing sheet with id=AE1, first strand: chain 'O' and resid 126 through 131 removed outlier: 3.718A pdb=" N ARG O 135 " --> pdb=" O ARG O 131 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 100 through 102 removed outlier: 5.974A pdb=" N ALA P 80 " --> pdb=" O CYS P 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 28 through 34 removed outlier: 3.567A pdb=" N TYR Q 63 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG Q 15 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 93 through 99 removed outlier: 7.037A pdb=" N ASN Q 77 " --> pdb=" O GLU Q 131 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU Q 131 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY Q 79 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL Q 129 " --> pdb=" O GLY Q 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP Q 81 " --> pdb=" O MET Q 127 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 84 through 92 removed outlier: 6.188A pdb=" N ILE R 75 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL R 64 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN R 77 " --> pdb=" O GLY R 62 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLY R 62 " --> pdb=" O ASN R 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'S' and resid 100 through 104 removed outlier: 3.637A pdb=" N ARG S 113 " --> pdb=" O ARG S 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 25 through 28 removed outlier: 6.866A pdb=" N MET T 62 " --> pdb=" O ILE T 40 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL T 42 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N MET T 60 " --> pdb=" O VAL T 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA T 102 " --> pdb=" O ILE T 82 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY T 103 " --> pdb=" O VAL T 25 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN T 27 " --> pdb=" O GLY T 103 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE T 105 " --> pdb=" O ASN T 27 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 88 through 89 removed outlier: 3.605A pdb=" N LEU T 96 " --> pdb=" O TYR T 88 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE T 95 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA U 22 " --> pdb=" O PHE T 95 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR T 97 " --> pdb=" O ALA U 22 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 4 through 5 removed outlier: 3.782A pdb=" N GLU U 4 " --> pdb=" O ILE U 13 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 77 through 80 removed outlier: 3.583A pdb=" N PHE V 79 " --> pdb=" O ILE V 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS V 134 " --> pdb=" O VAL V 100 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS V 135 " --> pdb=" O THR V 126 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR V 126 " --> pdb=" O LYS V 135 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR V 137 " --> pdb=" O VAL V 124 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL V 124 " --> pdb=" O TYR V 137 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG V 139 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 31 through 33 Processing sheet with id=AF4, first strand: chain 'W' and resid 79 through 82 removed outlier: 6.713A pdb=" N VAL W 79 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL W 73 " --> pdb=" O VAL W 79 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR W 81 " --> pdb=" O VAL W 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 86 through 88 Processing sheet with id=AF6, first strand: chain 'X' and resid 69 through 76 removed outlier: 6.637A pdb=" N LYS X 69 " --> pdb=" O ASP X 47 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS X 40 " --> pdb=" O ASN X 28 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN X 28 " --> pdb=" O HIS X 40 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU X 42 " --> pdb=" O VAL X 26 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE X 25 " --> pdb=" O LYS X 9 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS X 9 " --> pdb=" O ILE X 25 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR X 85 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU X 12 " --> pdb=" O THR X 83 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR X 83 " --> pdb=" O LEU X 12 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 72 through 74 removed outlier: 6.042A pdb=" N VAL Y 73 " --> pdb=" O LEU Y 112 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 26 through 29 removed outlier: 7.183A pdb=" N VAL a 28 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE a 96 " --> pdb=" O VAL a 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU a 45 " --> pdb=" O ILE a 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.995A pdb=" N ASP b 61 " --> pdb=" O THR b 104 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL b 106 " --> pdb=" O ASP b 61 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG b 63 " --> pdb=" O VAL b 106 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TYR b 108 " --> pdb=" O ARG b 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR b 22 " --> pdb=" O VAL b 122 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 75 through 79 removed outlier: 5.989A pdb=" N ARG c 75 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU c 98 " --> pdb=" O ARG c 75 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE c 77 " --> pdb=" O GLU c 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'd' and resid 9 through 16 removed outlier: 3.649A pdb=" N ALA d 12 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU d 27 " --> pdb=" O ALA d 12 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR d 14 " --> pdb=" O THR d 25 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR d 25 " --> pdb=" O TYR d 14 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ARG d 16 " --> pdb=" O GLU d 23 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N GLU d 23 " --> pdb=" O ARG d 16 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS d 24 " --> pdb=" O PHE d 88 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE d 88 " --> pdb=" O HIS d 24 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG d 76 " --> pdb=" O ARG d 85 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS d 87 " --> pdb=" O VAL d 74 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL d 74 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR d 67 " --> pdb=" O ASN d 55 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASN d 55 " --> pdb=" O THR d 67 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N VAL d 69 " --> pdb=" O ALA d 53 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N ALA d 53 " --> pdb=" O VAL d 69 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N TRP d 71 " --> pdb=" O TYR d 51 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N TYR d 51 " --> pdb=" O TRP d 71 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N LYS d 73 " --> pdb=" O TYR d 49 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N TYR d 49 " --> pdb=" O LYS d 73 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N THR d 75 " --> pdb=" O CYS d 47 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N CYS d 47 " --> pdb=" O THR d 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 20 through 25 removed outlier: 4.137A pdb=" N ARG e 29 " --> pdb=" O THR e 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 16 through 17 removed outlier: 3.541A pdb=" N TYR h 27 " --> pdb=" O THR h 17 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 3 through 4 removed outlier: 6.480A pdb=" N ARG i 3 " --> pdb=" O THR i 44 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL i 46 " --> pdb=" O ARG i 3 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER i 22 " --> pdb=" O ARG i 37 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL i 23 " --> pdb=" O LYS i 67 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 102 through 103 Processing sheet with id=AG7, first strand: chain 'm' and resid 7 through 12 removed outlier: 3.602A pdb=" N LYS m 17 " --> pdb=" O CYS m 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE m 66 " --> pdb=" O ILE m 85 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'o' and resid 22 through 24 Processing sheet with id=AG9, first strand: chain 'p' and resid 49 through 53 Processing sheet with id=AH1, first strand: chain 't' and resid 76 through 82 removed outlier: 6.216A pdb=" N GLY t 111 " --> pdb=" O PRO t 77 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 't' and resid 180 through 181 Processing sheet with id=AH3, first strand: chain 't' and resid 246 through 249 removed outlier: 4.353A pdb=" N ILE t 246 " --> pdb=" O PHE t 305 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2556 hydrogen bonds 4474 hydrogen bond angles 0 basepair planarities 967 basepair parallelities 1996 stacking parallelities Total time for adding SS restraints: 243.95 Time building geometry restraints manager: 57.72 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: 25005 1.33 - 1.45: 56532 1.45 - 1.57: 59083 1.57 - 1.69: 7762 1.69 - 1.81: 400 Bond restraints: 148782 Sorted by residual: bond pdb=" CA THR t 279 " pdb=" C THR t 279 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.18e-02 7.18e+03 6.51e+00 bond pdb=" C LEU t 325 " pdb=" O LEU t 325 " ideal model delta sigma weight residual 1.237 1.216 0.020 1.19e-02 7.06e+03 2.94e+00 bond pdb=" C ILE k 95 " pdb=" O ILE k 95 " ideal model delta sigma weight residual 1.238 1.219 0.018 1.09e-02 8.42e+03 2.82e+00 bond pdb=" N MET t 326 " pdb=" CA MET t 326 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.41e-02 5.03e+03 2.76e+00 bond pdb=" N TYR W 74 " pdb=" CA TYR W 74 " ideal model delta sigma weight residual 1.463 1.442 0.021 1.28e-02 6.10e+03 2.62e+00 ... (remaining 148777 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.62: 24032 106.62 - 113.47: 86999 113.47 - 120.31: 56062 120.31 - 127.16: 44010 127.16 - 134.00: 8588 Bond angle restraints: 219691 Sorted by residual: angle pdb=" N ALA t 140 " pdb=" CA ALA t 140 " pdb=" C ALA t 140 " ideal model delta sigma weight residual 111.28 102.62 8.66 1.09e+00 8.42e-01 6.32e+01 angle pdb=" C PHE t 76 " pdb=" N PRO t 77 " pdb=" CA PRO t 77 " ideal model delta sigma weight residual 119.84 129.61 -9.77 1.25e+00 6.40e-01 6.11e+01 angle pdb=" N ASP t 212 " pdb=" CA ASP t 212 " pdb=" C ASP t 212 " ideal model delta sigma weight residual 112.89 104.52 8.37 1.24e+00 6.50e-01 4.55e+01 angle pdb=" C THR t 136 " pdb=" CA THR t 136 " pdb=" CB THR t 136 " ideal model delta sigma weight residual 114.40 107.01 7.39 1.25e+00 6.40e-01 3.50e+01 angle pdb=" N ILE t 246 " pdb=" CA ILE t 246 " pdb=" C ILE t 246 " ideal model delta sigma weight residual 107.73 116.44 -8.71 1.56e+00 4.11e-01 3.12e+01 ... (remaining 219686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 85577 35.91 - 71.82: 9509 71.82 - 107.73: 1235 107.73 - 143.64: 6 143.64 - 179.55: 30 Dihedral angle restraints: 96357 sinusoidal: 76857 harmonic: 19500 Sorted by residual: dihedral pdb=" O4' U q1930 " pdb=" C1' U q1930 " pdb=" N1 U q1930 " pdb=" C2 U q1930 " ideal model delta sinusoidal sigma weight residual -160.00 12.42 -172.42 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C q2727 " pdb=" C1' C q2727 " pdb=" N1 C q2727 " pdb=" C2 C q2727 " ideal model delta sinusoidal sigma weight residual 200.00 28.18 171.82 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C q 219 " pdb=" C1' C q 219 " pdb=" N1 C q 219 " pdb=" C2 C q 219 " ideal model delta sinusoidal sigma weight residual 200.00 29.83 170.17 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 96354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 26095 0.062 - 0.125: 1221 0.125 - 0.187: 73 0.187 - 0.250: 13 0.250 - 0.312: 6 Chirality restraints: 27408 Sorted by residual: chirality pdb=" CA CYS k 99 " pdb=" N CYS k 99 " pdb=" C CYS k 99 " pdb=" CB CYS k 99 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA TRP h 49 " pdb=" N TRP h 49 " pdb=" C TRP h 49 " pdb=" CB TRP h 49 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1' U q4264 " pdb=" O4' U q4264 " pdb=" C2' U q4264 " pdb=" N1 U q4264 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 27405 not shown) Planarity restraints: 13321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 128 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C MET H 128 " 0.048 2.00e-02 2.50e+03 pdb=" O MET H 128 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG H 129 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C q4265 " 0.007 2.00e-02 2.50e+03 1.81e-02 7.38e+00 pdb=" N1 C q4265 " -0.016 2.00e-02 2.50e+03 pdb=" C2 C q4265 " 0.009 2.00e-02 2.50e+03 pdb=" O2 C q4265 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C q4265 " -0.021 2.00e-02 2.50e+03 pdb=" C4 C q4265 " 0.043 2.00e-02 2.50e+03 pdb=" N4 C q4265 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C q4265 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C q4265 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G q4723 " 0.035 2.00e-02 2.50e+03 1.48e-02 6.57e+00 pdb=" N9 G q4723 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G q4723 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G q4723 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G q4723 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G q4723 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G q4723 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G q4723 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G q4723 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G q4723 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G q4723 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G q4723 " -0.004 2.00e-02 2.50e+03 ... (remaining 13318 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 24 1.87 - 2.63: 3399 2.63 - 3.39: 171562 3.39 - 4.14: 418904 4.14 - 4.90: 620848 Nonbonded interactions: 1214737 Sorted by model distance: nonbonded pdb=" O LYS t 101 " pdb=" OD1 ASP t 104 " model vdw 1.115 3.040 nonbonded pdb=" N GLY t 73 " pdb=" CE1 HIS t 113 " model vdw 1.160 3.340 nonbonded pdb=" CB ALA t 75 " pdb=" O GLY t 111 " model vdw 1.200 3.460 nonbonded pdb=" OE1 GLN t 10 " pdb=" NE2 GLN t 192 " model vdw 1.226 2.520 nonbonded pdb=" OE1 GLN t 134 " pdb=" CG LYS t 344 " model vdw 1.375 3.440 ... (remaining 1214732 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.110 Extract box with map and model: 14.400 Check model and map are aligned: 1.460 Set scattering table: 0.920 Process input model: 505.170 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.320 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 529.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 0.033 148782 Z= 0.112 Angle : 0.451 10.537 219691 Z= 0.261 Chirality : 0.028 0.312 27408 Planarity : 0.003 0.059 13321 Dihedral : 22.578 179.546 83769 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.24 % Favored : 95.56 % Rotamer: Outliers : 0.43 % Allowed : 4.05 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: -2.39 (0.09), residues: 6651 helix: -0.88 (0.10), residues: 2140 sheet: -1.48 (0.15), residues: 914 loop : -2.09 (0.09), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP h 49 HIS 0.006 0.000 HIS O 25 PHE 0.018 0.001 PHE t 278 TYR 0.012 0.001 TYR M 62 ARG 0.004 0.000 ARG F 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2443 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 2418 time to evaluate : 6.584 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: A 87 PHE cc_start: 0.9065 (m-10) cc_final: 0.8784 (m-80) REVERT: A 96 LEU cc_start: 0.9108 (tt) cc_final: 0.8863 (tt) REVERT: B 53 MET cc_start: 0.8222 (mtp) cc_final: 0.7746 (mtp) REVERT: B 121 ASN cc_start: 0.8721 (t0) cc_final: 0.8212 (t0) REVERT: B 328 ASN cc_start: 0.7994 (m-40) cc_final: 0.7744 (m110) REVERT: C 50 GLN cc_start: 0.8756 (mt0) cc_final: 0.8443 (mt0) REVERT: C 108 TRP cc_start: 0.9206 (p90) cc_final: 0.8877 (p90) REVERT: C 204 ARG cc_start: 0.7302 (ptm160) cc_final: 0.7072 (mtp-110) REVERT: C 213 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6718 (tm-30) REVERT: C 218 ILE cc_start: 0.8443 (mm) cc_final: 0.8134 (mm) REVERT: C 300 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8158 (ttm-80) REVERT: C 337 ARG cc_start: 0.7076 (ptp-170) cc_final: 0.6641 (ttt180) REVERT: D 111 ASN cc_start: 0.8687 (t0) cc_final: 0.8352 (m-40) REVERT: D 122 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7566 (tt0) REVERT: D 177 THR cc_start: 0.8520 (p) cc_final: 0.8294 (m) REVERT: E 115 TYR cc_start: 0.8097 (t80) cc_final: 0.7788 (t80) REVERT: E 205 ASP cc_start: 0.7992 (p0) cc_final: 0.7441 (p0) REVERT: E 216 TYR cc_start: 0.9009 (t80) cc_final: 0.8725 (t80) REVERT: E 274 GLN cc_start: 0.8811 (mt0) cc_final: 0.8436 (mt0) REVERT: E 282 TYR cc_start: 0.8557 (m-80) cc_final: 0.8343 (m-80) REVERT: F 169 LEU cc_start: 0.9062 (mt) cc_final: 0.8793 (mt) REVERT: F 247 MET cc_start: 0.8828 (mmm) cc_final: 0.8373 (ttm) REVERT: G 75 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8221 (mtpp) REVERT: G 82 GLN cc_start: 0.8925 (mt0) cc_final: 0.8634 (mt0) REVERT: G 94 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8533 (tm-30) REVERT: G 208 ASN cc_start: 0.8083 (m-40) cc_final: 0.7118 (m-40) REVERT: G 211 ASP cc_start: 0.8573 (m-30) cc_final: 0.8182 (m-30) REVERT: G 226 TYR cc_start: 0.9051 (m-80) cc_final: 0.8800 (m-10) REVERT: H 5 LEU cc_start: 0.9324 (tp) cc_final: 0.9013 (tp) REVERT: H 92 MET cc_start: 0.8168 (mtp) cc_final: 0.7824 (mtm) REVERT: I 74 LYS cc_start: 0.8534 (tppp) cc_final: 0.8063 (mtpt) REVERT: I 150 GLU cc_start: 0.8334 (tp30) cc_final: 0.8100 (tp30) REVERT: I 166 HIS cc_start: 0.7915 (t-90) cc_final: 0.7622 (t-170) REVERT: I 182 GLU cc_start: 0.7881 (pm20) cc_final: 0.7679 (pm20) REVERT: J 84 GLU cc_start: 0.8779 (tm-30) cc_final: 0.7658 (tp30) REVERT: J 88 LYS cc_start: 0.8607 (tptm) cc_final: 0.8397 (tppt) REVERT: J 91 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7612 (mm-30) REVERT: J 126 TYR cc_start: 0.6746 (m-80) cc_final: 0.5950 (m-80) REVERT: J 140 SER cc_start: 0.9256 (m) cc_final: 0.8911 (t) REVERT: K 94 ILE cc_start: 0.9314 (mm) cc_final: 0.9092 (tp) REVERT: K 99 ASP cc_start: 0.8960 (t0) cc_final: 0.8245 (t0) REVERT: K 125 ILE cc_start: 0.7275 (mm) cc_final: 0.6809 (mm) REVERT: K 127 PHE cc_start: 0.8377 (m-10) cc_final: 0.8153 (m-80) REVERT: K 157 ILE cc_start: 0.8368 (mm) cc_final: 0.8046 (mm) REVERT: L 6 TYR cc_start: 0.8817 (m-80) cc_final: 0.7722 (m-80) REVERT: L 8 GLU cc_start: 0.8729 (pt0) cc_final: 0.8353 (pm20) REVERT: L 48 GLN cc_start: 0.8466 (pt0) cc_final: 0.8258 (pt0) REVERT: L 72 TYR cc_start: 0.8360 (m-80) cc_final: 0.8051 (m-80) REVERT: M 145 ASN cc_start: 0.8677 (t0) cc_final: 0.8097 (t0) REVERT: M 189 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8044 (mtt90) REVERT: M 193 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7400 (mtm-85) REVERT: N 50 ASN cc_start: 0.9160 (m-40) cc_final: 0.8697 (m-40) REVERT: N 118 MET cc_start: 0.8050 (mmt) cc_final: 0.7809 (mmm) REVERT: N 144 GLU cc_start: 0.7730 (tt0) cc_final: 0.7475 (tt0) REVERT: N 169 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7964 (mtp180) REVERT: O 126 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7094 (mtp85) REVERT: Q 174 THR cc_start: 0.8284 (m) cc_final: 0.8046 (p) REVERT: R 108 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7765 (ttp-110) REVERT: S 25 CYS cc_start: 0.8318 (t) cc_final: 0.7864 (t) REVERT: S 30 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7932 (pt0) REVERT: T 35 LYS cc_start: 0.8444 (mttp) cc_final: 0.8176 (mmpt) REVERT: U 8 PHE cc_start: 0.9002 (t80) cc_final: 0.8780 (t80) REVERT: U 12 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8891 (mtpp) REVERT: V 55 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7798 (tpt170) REVERT: V 69 ASN cc_start: 0.8958 (t0) cc_final: 0.8756 (t0) REVERT: V 87 MET cc_start: 0.8090 (mmt) cc_final: 0.7675 (mmt) REVERT: V 145 ASP cc_start: 0.8178 (t0) cc_final: 0.7877 (t70) REVERT: W 47 MET cc_start: 0.8965 (tpt) cc_final: 0.8613 (tpt) REVERT: W 73 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8823 (p) REVERT: W 120 GLU cc_start: 0.7834 (pp20) cc_final: 0.7620 (pp20) REVERT: X 52 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8417 (tptt) REVERT: X 111 ARG cc_start: 0.9006 (ttm110) cc_final: 0.8747 (mtp-110) REVERT: Y 48 TYR cc_start: 0.8803 (m-80) cc_final: 0.8448 (m-80) REVERT: Y 108 TYR cc_start: 0.9016 (m-80) cc_final: 0.8647 (m-80) REVERT: Y 120 GLN cc_start: 0.8369 (mt0) cc_final: 0.8149 (mt0) REVERT: Y 134 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7224 (tm-30) REVERT: a 57 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8677 (ttmt) REVERT: a 72 HIS cc_start: 0.8385 (t70) cc_final: 0.7888 (t-90) REVERT: a 81 LEU cc_start: 0.8898 (tp) cc_final: 0.8458 (tp) REVERT: b 25 TYR cc_start: 0.8920 (m-80) cc_final: 0.8456 (m-80) REVERT: b 40 LYS cc_start: 0.7719 (mttm) cc_final: 0.7200 (mtmm) REVERT: b 54 MET cc_start: 0.8294 (mmt) cc_final: 0.8076 (mmm) REVERT: b 59 THR cc_start: 0.8352 (p) cc_final: 0.8043 (t) REVERT: b 101 LYS cc_start: 0.8285 (mttp) cc_final: 0.8079 (mmtt) REVERT: c 37 LYS cc_start: 0.8718 (tptm) cc_final: 0.8490 (tptp) REVERT: c 52 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8172 (mm110) REVERT: c 57 ASN cc_start: 0.9075 (p0) cc_final: 0.8818 (p0) REVERT: c 70 LEU cc_start: 0.9052 (mp) cc_final: 0.8835 (mt) REVERT: c 92 ASN cc_start: 0.8805 (p0) cc_final: 0.8498 (p0) REVERT: e 34 TYR cc_start: 0.8929 (m-80) cc_final: 0.8678 (m-80) REVERT: e 99 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8371 (mm-30) REVERT: e 100 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8400 (tp-100) REVERT: e 104 VAL cc_start: 0.8719 (p) cc_final: 0.8491 (p) REVERT: f 7 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7730 (ttp80) REVERT: f 108 GLN cc_start: 0.8714 (mt0) cc_final: 0.8356 (mt0) REVERT: g 59 GLU cc_start: 0.8035 (tp30) cc_final: 0.7768 (tp30) REVERT: g 70 LEU cc_start: 0.9155 (tp) cc_final: 0.8839 (tp) REVERT: g 75 LYS cc_start: 0.9144 (tppt) cc_final: 0.8573 (tttm) REVERT: g 88 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8309 (mm-30) REVERT: h 8 PHE cc_start: 0.9039 (m-10) cc_final: 0.8771 (m-80) REVERT: i 16 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8556 (ttp-110) REVERT: j 35 ILE cc_start: 0.9395 (mt) cc_final: 0.9167 (mt) REVERT: k 109 ASN cc_start: 0.9034 (m-40) cc_final: 0.8558 (m-40) REVERT: k 114 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7778 (ptmt) REVERT: l 2 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7187 (tpp-160) REVERT: l 4 LYS cc_start: 0.8242 (tttt) cc_final: 0.6651 (mmtt) REVERT: l 10 MET cc_start: 0.8375 (tpt) cc_final: 0.8070 (tpp) REVERT: l 15 ARG cc_start: 0.8060 (ptt180) cc_final: 0.7761 (mtt-85) REVERT: l 17 ARG cc_start: 0.8537 (ttm170) cc_final: 0.8179 (mtm-85) REVERT: l 19 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8886 (ttpt) REVERT: l 21 ARG cc_start: 0.8020 (tpt-90) cc_final: 0.6580 (tpt170) REVERT: m 92 GLU cc_start: 0.8122 (tt0) cc_final: 0.7799 (tm-30) REVERT: n 6 LYS cc_start: 0.8579 (tptt) cc_final: 0.7987 (tptp) REVERT: n 28 LYS cc_start: 0.8472 (tttp) cc_final: 0.8260 (ttpp) REVERT: n 79 VAL cc_start: 0.9188 (t) cc_final: 0.8914 (t) REVERT: n 83 ILE cc_start: 0.9098 (mt) cc_final: 0.8865 (mt) REVERT: o 7 GLN cc_start: 0.8777 (mp10) cc_final: 0.8536 (mp10) REVERT: o 144 LYS cc_start: 0.8413 (tptt) cc_final: 0.8188 (tppt) REVERT: p 36 ASN cc_start: 0.9152 (t0) cc_final: 0.8802 (t0) REVERT: p 102 TYR cc_start: 0.8029 (t80) cc_final: 0.7782 (t80) REVERT: t 9 GLU cc_start: 0.6372 (tm-30) cc_final: 0.6114 (tm-30) REVERT: t 110 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7811 (pp) REVERT: t 182 ILE cc_start: 0.8630 (mm) cc_final: 0.8095 (mm) REVERT: t 218 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.4360 (m-80) REVERT: t 291 MET cc_start: 0.8475 (tmm) cc_final: 0.8216 (tmm) REVERT: t 303 GLN cc_start: 0.8342 (mt0) cc_final: 0.7793 (mp10) REVERT: t 321 PHE cc_start: 0.7418 (p90) cc_final: 0.6526 (p90) outliers start: 25 outliers final: 14 residues processed: 2439 average time/residue: 1.3700 time to fit residues: 5506.1747 Evaluate side-chains 1778 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1761 time to evaluate : 8.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 49 CYS Chi-restraints excluded: chain t residue 85 CYS Chi-restraints excluded: chain t residue 104 ASP Chi-restraints excluded: chain t residue 110 LEU Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 113 HIS Chi-restraints excluded: chain t residue 196 ASP Chi-restraints excluded: chain t residue 201 ILE Chi-restraints excluded: chain t residue 218 PHE Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 878 optimal weight: 10.0000 chunk 788 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 531 optimal weight: 8.9990 chunk 421 optimal weight: 3.9990 chunk 815 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 495 optimal weight: 4.9990 chunk 606 optimal weight: 7.9990 chunk 944 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 218 HIS B 158 GLN B 179 HIS B 213 GLN B 245 HIS C 43 ASN C 89 GLN C 94 ASN C 215 ASN C 338 ASN C 343 GLN C 346 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 222 GLN D 225 GLN D 291 GLN E 128 HIS E 135 GLN E 190 HIS E 191 GLN E 211 HIS E 221 GLN F 116 GLN F 206 ASN F 241 ASN G 43 GLN G 195 HIS H 108 ASN H 156 ASN H 188 GLN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 HIS I 86 HIS I 123 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS ** K 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 120 ASN M 37 HIS M 86 HIS M 87 HIS M 109 HIS M 145 ASN M 181 HIS M 196 ASN M 201 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN O 10 ASN O 34 GLN O 56 GLN P 77 ASN Q 66 GLN Q 92 ASN Q 108 GLN Q 122 HIS S 27 HIS S 44 GLN T 101 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 ASN W 72 GLN Y 66 ASN Y 74 ASN Z 19 ASN Z 49 HIS Z 61 ASN a 33 GLN ** a 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 18 ASN c 107 ASN ** d 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN g 15 HIS g 92 ASN h 48 ASN h 57 ASN j 25 GLN j 43 HIS k 84 GLN k 104 HIS m 18 HIS m 45 GLN n 33 GLN o 40 GLN o 58 HIS p 45 HIS t 8 GLN ** t 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 254 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 148782 Z= 0.456 Angle : 0.677 14.683 219691 Z= 0.340 Chirality : 0.039 0.299 27408 Planarity : 0.006 0.111 13321 Dihedral : 23.620 179.972 69334 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.05 % Favored : 94.93 % Rotamer: Outliers : 4.93 % Allowed : 16.42 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 6651 helix: 0.05 (0.11), residues: 2185 sheet: -1.18 (0.16), residues: 946 loop : -1.59 (0.10), residues: 3520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 266 HIS 0.012 0.002 HIS O 25 PHE 0.022 0.002 PHE F 37 TYR 0.029 0.002 TYR S 85 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2030 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1744 time to evaluate : 6.707 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: A 48 ILE cc_start: 0.8858 (pt) cc_final: 0.8571 (mt) REVERT: A 65 ASP cc_start: 0.8651 (t0) cc_final: 0.8266 (t0) REVERT: A 95 GLN cc_start: 0.8366 (mp10) cc_final: 0.8138 (mp10) REVERT: A 96 LEU cc_start: 0.9149 (tt) cc_final: 0.8930 (tt) REVERT: B 53 MET cc_start: 0.8322 (mtp) cc_final: 0.7968 (mtp) REVERT: B 97 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8081 (mtt180) REVERT: B 121 ASN cc_start: 0.8695 (t0) cc_final: 0.8300 (t0) REVERT: B 216 MET cc_start: 0.9103 (mmt) cc_final: 0.8467 (mmt) REVERT: B 258 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: B 328 ASN cc_start: 0.7969 (m-40) cc_final: 0.7633 (m110) REVERT: C 201 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8272 (mmm-85) REVERT: D 111 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8362 (m-40) REVERT: E 115 TYR cc_start: 0.8276 (t80) cc_final: 0.7889 (t80) REVERT: E 205 ASP cc_start: 0.8197 (p0) cc_final: 0.7490 (p0) REVERT: E 245 GLN cc_start: 0.7704 (tp40) cc_final: 0.7489 (tp40) REVERT: E 274 GLN cc_start: 0.8778 (mt0) cc_final: 0.8513 (mt0) REVERT: F 110 GLN cc_start: 0.9030 (mt0) cc_final: 0.8825 (mt0) REVERT: F 115 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.8020 (mmt180) REVERT: F 142 TRP cc_start: 0.9076 (p-90) cc_final: 0.8820 (p-90) REVERT: F 169 LEU cc_start: 0.9262 (mt) cc_final: 0.9055 (mt) REVERT: F 193 GLU cc_start: 0.8395 (tp30) cc_final: 0.7965 (tp30) REVERT: F 247 MET cc_start: 0.8946 (mmm) cc_final: 0.8423 (ttm) REVERT: G 75 LYS cc_start: 0.8653 (mtmt) cc_final: 0.7974 (mtpp) REVERT: G 109 GLU cc_start: 0.8643 (pt0) cc_final: 0.8017 (pp20) REVERT: G 167 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9129 (t) REVERT: G 211 ASP cc_start: 0.8369 (m-30) cc_final: 0.7995 (m-30) REVERT: G 226 TYR cc_start: 0.9189 (m-80) cc_final: 0.8984 (m-10) REVERT: G 228 ASP cc_start: 0.8423 (t0) cc_final: 0.8192 (t0) REVERT: G 240 ASN cc_start: 0.9012 (t0) cc_final: 0.8518 (t0) REVERT: H 5 LEU cc_start: 0.9168 (tp) cc_final: 0.8944 (tp) REVERT: H 92 MET cc_start: 0.8323 (mtp) cc_final: 0.7877 (mtm) REVERT: H 188 GLN cc_start: 0.8251 (mm110) cc_final: 0.8014 (mm-40) REVERT: I 11 TYR cc_start: 0.8240 (m-80) cc_final: 0.7896 (m-10) REVERT: I 116 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7421 (ttm170) REVERT: I 123 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: I 166 HIS cc_start: 0.8176 (t-90) cc_final: 0.7870 (t-170) REVERT: J 140 SER cc_start: 0.9492 (m) cc_final: 0.9179 (t) REVERT: J 168 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8415 (tm-30) REVERT: K 19 GLN cc_start: 0.8966 (mt0) cc_final: 0.8766 (mt0) REVERT: K 35 ARG cc_start: 0.8544 (mtt180) cc_final: 0.8191 (mtt90) REVERT: K 99 ASP cc_start: 0.9153 (t0) cc_final: 0.8743 (t0) REVERT: K 157 ILE cc_start: 0.8669 (mm) cc_final: 0.8348 (mm) REVERT: K 177 LYS cc_start: 0.6961 (mmmm) cc_final: 0.6543 (mmmm) REVERT: L 8 GLU cc_start: 0.8907 (pt0) cc_final: 0.8702 (pt0) REVERT: M 12 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8380 (mtt180) REVERT: M 145 ASN cc_start: 0.8813 (t0) cc_final: 0.8244 (t0) REVERT: M 160 GLU cc_start: 0.7939 (pm20) cc_final: 0.6696 (pm20) REVERT: M 189 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8053 (mtt90) REVERT: M 193 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7326 (mtt90) REVERT: M 203 TYR cc_start: 0.8954 (m-80) cc_final: 0.8707 (m-80) REVERT: N 39 GLU cc_start: 0.8618 (pm20) cc_final: 0.8220 (pm20) REVERT: N 54 TYR cc_start: 0.8850 (t80) cc_final: 0.8407 (t80) REVERT: N 100 GLU cc_start: 0.8547 (mp0) cc_final: 0.8050 (mp0) REVERT: N 137 TYR cc_start: 0.8516 (m-80) cc_final: 0.8147 (m-80) REVERT: N 169 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7961 (mtp180) REVERT: P 8 ASN cc_start: 0.8775 (p0) cc_final: 0.8568 (p0) REVERT: S 25 CYS cc_start: 0.8150 (t) cc_final: 0.7773 (t) REVERT: S 64 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6911 (tm-30) REVERT: S 93 LYS cc_start: 0.8967 (tmmt) cc_final: 0.8571 (tmmt) REVERT: S 94 ASN cc_start: 0.8930 (m-40) cc_final: 0.8290 (m-40) REVERT: S 99 TRP cc_start: 0.8573 (m-10) cc_final: 0.8372 (m-10) REVERT: S 108 GLU cc_start: 0.8179 (tt0) cc_final: 0.7901 (tp30) REVERT: T 85 ARG cc_start: 0.8764 (mtp85) cc_final: 0.8537 (mtp180) REVERT: U 11 TYR cc_start: 0.8588 (m-80) cc_final: 0.8252 (m-80) REVERT: V 69 ASN cc_start: 0.8986 (t0) cc_final: 0.8609 (t0) REVERT: V 145 ASP cc_start: 0.8195 (t0) cc_final: 0.7882 (t70) REVERT: W 62 TYR cc_start: 0.9251 (m-80) cc_final: 0.8911 (m-80) REVERT: W 120 GLU cc_start: 0.7797 (pp20) cc_final: 0.7568 (pp20) REVERT: X 67 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8468 (mmmm) REVERT: X 97 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8426 (p0) REVERT: X 113 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8796 (tp30) REVERT: Y 61 TYR cc_start: 0.9156 (m-80) cc_final: 0.8454 (m-80) REVERT: Y 75 LEU cc_start: 0.8984 (mm) cc_final: 0.8649 (mm) REVERT: Y 108 TYR cc_start: 0.9097 (m-80) cc_final: 0.8727 (m-80) REVERT: Y 120 GLN cc_start: 0.8627 (mt0) cc_final: 0.8322 (mt0) REVERT: Y 134 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7159 (tm-30) REVERT: Y 135 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6912 (mm-30) REVERT: Z 3 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8748 (ttmm) REVERT: Z 11 ASN cc_start: 0.8369 (t0) cc_final: 0.8061 (t0) REVERT: a 57 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8725 (ttmt) REVERT: a 72 HIS cc_start: 0.8506 (t70) cc_final: 0.8017 (t-90) REVERT: a 77 ASN cc_start: 0.9021 (p0) cc_final: 0.8691 (p0) REVERT: a 81 LEU cc_start: 0.8933 (tp) cc_final: 0.8723 (tp) REVERT: b 40 LYS cc_start: 0.8095 (mttm) cc_final: 0.7664 (mtmm) REVERT: b 59 THR cc_start: 0.8405 (p) cc_final: 0.8100 (t) REVERT: b 70 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8611 (mtpp) REVERT: b 79 ASN cc_start: 0.8528 (m-40) cc_final: 0.8197 (m-40) REVERT: b 101 LYS cc_start: 0.8329 (mttp) cc_final: 0.8125 (mmtt) REVERT: b 103 TYR cc_start: 0.8653 (p90) cc_final: 0.8252 (p90) REVERT: c 52 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8764 (mm-40) REVERT: c 57 ASN cc_start: 0.9186 (p0) cc_final: 0.8985 (p0) REVERT: c 70 LEU cc_start: 0.9086 (mp) cc_final: 0.8843 (mt) REVERT: c 86 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: e 29 ARG cc_start: 0.7636 (ptt-90) cc_final: 0.7241 (ptt-90) REVERT: e 100 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8415 (tp-100) REVERT: f 7 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7832 (ttp-170) REVERT: f 22 ASP cc_start: 0.8327 (t0) cc_final: 0.7845 (p0) REVERT: f 108 GLN cc_start: 0.8708 (mt0) cc_final: 0.8358 (mt0) REVERT: g 84 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8643 (mtpp) REVERT: i 16 ARG cc_start: 0.8871 (ptp90) cc_final: 0.8586 (ttm110) REVERT: i 58 GLN cc_start: 0.7819 (mp10) cc_final: 0.7560 (mp10) REVERT: j 15 LYS cc_start: 0.8802 (tttp) cc_final: 0.8258 (tttp) REVERT: j 36 ARG cc_start: 0.7343 (mtt90) cc_final: 0.7135 (mtt180) REVERT: k 114 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7881 (ptpt) REVERT: l 2 ARG cc_start: 0.8605 (ttt180) cc_final: 0.7616 (ttm170) REVERT: l 4 LYS cc_start: 0.8565 (tttt) cc_final: 0.6845 (mmtt) REVERT: l 15 ARG cc_start: 0.8306 (ptt180) cc_final: 0.7816 (mtt-85) REVERT: l 19 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8885 (ttpt) REVERT: l 21 ARG cc_start: 0.8360 (tpt-90) cc_final: 0.6737 (tpt170) REVERT: n 6 LYS cc_start: 0.8665 (tptt) cc_final: 0.8201 (tptt) REVERT: n 28 LYS cc_start: 0.8693 (tttp) cc_final: 0.8344 (ttpp) REVERT: n 31 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8306 (pt) REVERT: n 79 VAL cc_start: 0.9430 (t) cc_final: 0.9203 (t) REVERT: n 83 ILE cc_start: 0.9206 (mt) cc_final: 0.8976 (mt) REVERT: o 25 ASP cc_start: 0.8106 (t70) cc_final: 0.7739 (t70) REVERT: o 86 ASN cc_start: 0.9033 (t0) cc_final: 0.8703 (t0) REVERT: o 149 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8114 (tptp) REVERT: p 28 GLU cc_start: 0.7964 (mp0) cc_final: 0.7556 (mp0) REVERT: t 182 ILE cc_start: 0.8586 (mm) cc_final: 0.7722 (mm) REVERT: t 185 MET cc_start: 0.7916 (mmp) cc_final: 0.7291 (mmp) REVERT: t 218 PHE cc_start: 0.5360 (OUTLIER) cc_final: 0.4441 (m-80) REVERT: t 221 HIS cc_start: 0.7576 (m90) cc_final: 0.7375 (m-70) outliers start: 286 outliers final: 211 residues processed: 1879 average time/residue: 1.3115 time to fit residues: 4272.8622 Evaluate side-chains 1837 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1615 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 132 ILE Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 82 ILE Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 ILE Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 69 LYS Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 66 SER Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 97 ASN Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain a residue 14 ILE Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 75 SER Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 56 ASN Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 15 THR Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain i residue 9 LYS Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 91 SER Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 134 GLN Chi-restraints excluded: chain t residue 171 ASN Chi-restraints excluded: chain t residue 218 PHE Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 291 MET Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 524 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 786 optimal weight: 8.9990 chunk 643 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 946 optimal weight: 7.9990 chunk 1022 optimal weight: 6.9990 chunk 842 optimal weight: 7.9990 chunk 938 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 759 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 167 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 191 GLN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN L 48 GLN M 37 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN O 10 ASN O 145 HIS ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN R 139 HIS ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS Y 66 ASN Y 89 ASN a 50 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 ASN c 107 ASN d 78 HIS f 63 GLN g 92 ASN m 19 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN ** t 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 193 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 148782 Z= 0.333 Angle : 0.588 13.310 219691 Z= 0.299 Chirality : 0.036 0.275 27408 Planarity : 0.005 0.096 13321 Dihedral : 23.580 179.802 69315 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.60 % Allowed : 18.97 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 6651 helix: 0.52 (0.11), residues: 2184 sheet: -1.16 (0.16), residues: 939 loop : -1.32 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 266 HIS 0.027 0.001 HIS S 27 PHE 0.030 0.002 PHE X 131 TYR 0.027 0.002 TYR e 32 ARG 0.008 0.001 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2027 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1702 time to evaluate : 6.697 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: A 48 ILE cc_start: 0.8865 (pt) cc_final: 0.8649 (mt) REVERT: A 65 ASP cc_start: 0.8662 (t0) cc_final: 0.8314 (t0) REVERT: A 194 ASN cc_start: 0.8976 (t0) cc_final: 0.8560 (t0) REVERT: B 53 MET cc_start: 0.8321 (mtp) cc_final: 0.7972 (mtp) REVERT: B 69 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8255 (mttt) REVERT: B 97 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8176 (mtt180) REVERT: B 121 ASN cc_start: 0.8769 (t0) cc_final: 0.8293 (t0) REVERT: B 258 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.7925 (t-90) REVERT: B 328 ASN cc_start: 0.7947 (m-40) cc_final: 0.7649 (m110) REVERT: B 332 MET cc_start: 0.7958 (ttm) cc_final: 0.7450 (ttt) REVERT: C 13 GLU cc_start: 0.8429 (pp20) cc_final: 0.8131 (pp20) REVERT: C 20 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8403 (mmmt) REVERT: C 201 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8305 (mmm-85) REVERT: D 111 ASN cc_start: 0.8707 (t0) cc_final: 0.8335 (m-40) REVERT: D 152 ARG cc_start: 0.8710 (tpt170) cc_final: 0.8379 (tpt170) REVERT: E 115 TYR cc_start: 0.8268 (t80) cc_final: 0.7273 (t80) REVERT: E 205 ASP cc_start: 0.8040 (p0) cc_final: 0.7726 (p0) REVERT: E 274 GLN cc_start: 0.8745 (mt0) cc_final: 0.8476 (mt0) REVERT: F 193 GLU cc_start: 0.8305 (tp30) cc_final: 0.7884 (tp30) REVERT: F 247 MET cc_start: 0.8943 (mmm) cc_final: 0.8381 (ttm) REVERT: G 74 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8649 (mm) REVERT: G 75 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8009 (mtpp) REVERT: G 150 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8560 (mmtm) REVERT: G 167 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9184 (t) REVERT: G 211 ASP cc_start: 0.8418 (m-30) cc_final: 0.8028 (m-30) REVERT: G 228 ASP cc_start: 0.8390 (t0) cc_final: 0.8159 (t0) REVERT: G 240 ASN cc_start: 0.9020 (t0) cc_final: 0.8523 (t0) REVERT: H 5 LEU cc_start: 0.9127 (tp) cc_final: 0.8915 (tp) REVERT: H 8 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7361 (tm-30) REVERT: H 92 MET cc_start: 0.8285 (mtp) cc_final: 0.7904 (mtm) REVERT: I 116 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7571 (ttm170) REVERT: I 170 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8737 (mmmm) REVERT: J 66 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7129 (mt-10) REVERT: J 84 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8334 (tp30) REVERT: J 92 TYR cc_start: 0.8269 (m-10) cc_final: 0.7959 (m-10) REVERT: J 104 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8536 (m110) REVERT: J 140 SER cc_start: 0.9457 (m) cc_final: 0.9137 (t) REVERT: J 168 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8391 (tm-30) REVERT: K 17 ASP cc_start: 0.8713 (t0) cc_final: 0.8471 (t0) REVERT: K 99 ASP cc_start: 0.9129 (t0) cc_final: 0.8737 (t0) REVERT: K 119 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8453 (tm-30) REVERT: K 157 ILE cc_start: 0.8599 (mm) cc_final: 0.8268 (mm) REVERT: K 177 LYS cc_start: 0.7464 (mmmm) cc_final: 0.7257 (mmmm) REVERT: K 201 GLU cc_start: 0.8271 (pp20) cc_final: 0.7814 (tm-30) REVERT: L 6 TYR cc_start: 0.8967 (m-80) cc_final: 0.8485 (m-80) REVERT: M 12 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8440 (mtt180) REVERT: M 145 ASN cc_start: 0.8836 (t0) cc_final: 0.8308 (t0) REVERT: N 96 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: N 100 GLU cc_start: 0.8566 (mp0) cc_final: 0.8064 (mp0) REVERT: N 137 TYR cc_start: 0.8526 (m-80) cc_final: 0.8136 (m-80) REVERT: N 169 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7997 (mtm180) REVERT: P 6 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8520 (ptm-80) REVERT: P 14 ARG cc_start: 0.8212 (ptt90) cc_final: 0.7920 (ptt90) REVERT: P 17 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: Q 21 LYS cc_start: 0.8012 (pptt) cc_final: 0.7763 (pptt) REVERT: R 111 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7572 (tm-30) REVERT: S 25 CYS cc_start: 0.8173 (t) cc_final: 0.7482 (t) REVERT: S 34 MET cc_start: 0.8050 (ppp) cc_final: 0.7177 (ppp) REVERT: S 44 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7845 (pp30) REVERT: S 64 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6842 (tm-30) REVERT: S 108 GLU cc_start: 0.8077 (tt0) cc_final: 0.7798 (tp30) REVERT: T 35 LYS cc_start: 0.8423 (mmpt) cc_final: 0.7963 (mttp) REVERT: U 11 TYR cc_start: 0.8569 (m-80) cc_final: 0.8247 (m-80) REVERT: U 57 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7960 (ttp-110) REVERT: V 69 ASN cc_start: 0.9043 (t0) cc_final: 0.8676 (t0) REVERT: V 145 ASP cc_start: 0.8158 (t0) cc_final: 0.7890 (t70) REVERT: W 120 GLU cc_start: 0.7825 (pp20) cc_final: 0.7579 (pp20) REVERT: X 57 MET cc_start: 0.7816 (mtp) cc_final: 0.7413 (mtt) REVERT: X 67 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: X 80 LEU cc_start: 0.8694 (pp) cc_final: 0.8471 (pt) REVERT: X 97 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8662 (p0) REVERT: X 113 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8753 (tp30) REVERT: Y 48 TYR cc_start: 0.8936 (m-80) cc_final: 0.8583 (m-80) REVERT: Y 61 TYR cc_start: 0.9139 (m-80) cc_final: 0.8429 (m-80) REVERT: Y 108 TYR cc_start: 0.9111 (m-80) cc_final: 0.8701 (m-80) REVERT: Y 120 GLN cc_start: 0.8578 (mt0) cc_final: 0.8276 (mt0) REVERT: Y 134 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7603 (tm-30) REVERT: Z 3 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8601 (mtmm) REVERT: Z 11 ASN cc_start: 0.8332 (t0) cc_final: 0.8005 (t0) REVERT: a 57 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8694 (ttmt) REVERT: a 72 HIS cc_start: 0.8533 (t70) cc_final: 0.8191 (t-90) REVERT: b 40 LYS cc_start: 0.8055 (mttm) cc_final: 0.7627 (mtmm) REVERT: b 56 GLU cc_start: 0.8065 (tp30) cc_final: 0.7776 (tp30) REVERT: b 79 ASN cc_start: 0.8541 (m-40) cc_final: 0.8248 (m110) REVERT: b 103 TYR cc_start: 0.8679 (p90) cc_final: 0.8406 (p90) REVERT: c 52 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8743 (mm110) REVERT: c 70 LEU cc_start: 0.9055 (mp) cc_final: 0.8821 (mt) REVERT: c 86 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: d 50 VAL cc_start: 0.9313 (t) cc_final: 0.9008 (p) REVERT: e 100 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8222 (tp-100) REVERT: f 7 ARG cc_start: 0.8248 (ttt180) cc_final: 0.7839 (ttp-170) REVERT: f 108 GLN cc_start: 0.8680 (mt0) cc_final: 0.8343 (mt0) REVERT: g 43 MET cc_start: 0.7797 (tmm) cc_final: 0.7580 (tmm) REVERT: g 84 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8637 (mtpp) REVERT: g 98 GLU cc_start: 0.7678 (mp0) cc_final: 0.7244 (mp0) REVERT: i 3 ARG cc_start: 0.8423 (mmt180) cc_final: 0.8159 (mmt180) REVERT: i 16 ARG cc_start: 0.8903 (ptp90) cc_final: 0.8560 (ttm110) REVERT: i 58 GLN cc_start: 0.8032 (mp10) cc_final: 0.7690 (mp10) REVERT: k 114 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7945 (ptpt) REVERT: l 2 ARG cc_start: 0.8588 (ttt180) cc_final: 0.7574 (ttm170) REVERT: l 4 LYS cc_start: 0.8605 (tttt) cc_final: 0.6885 (mmtt) REVERT: l 10 MET cc_start: 0.8541 (tpp) cc_final: 0.8314 (tpp) REVERT: l 15 ARG cc_start: 0.8368 (ptt180) cc_final: 0.7960 (mtt-85) REVERT: l 19 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8881 (ttpt) REVERT: l 21 ARG cc_start: 0.8444 (tpt-90) cc_final: 0.6841 (tpt170) REVERT: m 19 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8193 (mm-40) REVERT: n 6 LYS cc_start: 0.8665 (tptt) cc_final: 0.8170 (tptt) REVERT: n 28 LYS cc_start: 0.8767 (tttp) cc_final: 0.8517 (ttpp) REVERT: n 83 ILE cc_start: 0.9193 (mt) cc_final: 0.8938 (mt) REVERT: n 84 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7808 (ptm160) REVERT: o 7 GLN cc_start: 0.9051 (mp10) cc_final: 0.8723 (mp10) REVERT: o 25 ASP cc_start: 0.8127 (t70) cc_final: 0.7724 (t70) REVERT: o 86 ASN cc_start: 0.9111 (t0) cc_final: 0.8862 (t0) REVERT: o 162 ARG cc_start: 0.6318 (ttm170) cc_final: 0.5847 (tmt170) REVERT: p 28 GLU cc_start: 0.7882 (mp0) cc_final: 0.7358 (mp0) REVERT: p 64 MET cc_start: 0.8634 (mtp) cc_final: 0.8280 (mtp) REVERT: t 175 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.8017 (m90) REVERT: t 259 MET cc_start: 0.7335 (mtp) cc_final: 0.6785 (ttm) REVERT: t 271 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8488 (ttp-110) outliers start: 325 outliers final: 251 residues processed: 1851 average time/residue: 1.3138 time to fit residues: 4260.3044 Evaluate side-chains 1889 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1623 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 56 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 90 ILE Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 97 ASN Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 56 ASN Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 91 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 15 THR Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain k residue 99 CYS Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 19 GLN Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 60 CYS Chi-restraints excluded: chain n residue 73 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 171 ASN Chi-restraints excluded: chain t residue 175 HIS Chi-restraints excluded: chain t residue 189 GLN Chi-restraints excluded: chain t residue 270 GLU Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 934 optimal weight: 8.9990 chunk 711 optimal weight: 8.9990 chunk 491 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 451 optimal weight: 7.9990 chunk 635 optimal weight: 20.0000 chunk 949 optimal weight: 8.9990 chunk 1005 optimal weight: 0.6980 chunk 496 optimal weight: 5.9990 chunk 899 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 50 HIS B 158 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 258 HIS C 38 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN D 63 GLN E 256 GLN F 206 ASN G 85 GLN G 149 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN M 37 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN O 10 ASN R 77 ASN S 94 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN a 72 HIS b 121 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 ASN f 107 GLN g 92 ASN m 19 GLN m 25 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN ** t 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 242 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 148782 Z= 0.240 Angle : 0.539 15.013 219691 Z= 0.274 Chirality : 0.033 0.266 27408 Planarity : 0.004 0.088 13321 Dihedral : 23.551 179.859 69312 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.57 % Allowed : 20.38 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.10), residues: 6651 helix: 0.78 (0.11), residues: 2195 sheet: -1.05 (0.16), residues: 939 loop : -1.10 (0.10), residues: 3517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 266 HIS 0.006 0.001 HIS Y 40 PHE 0.025 0.001 PHE X 131 TYR 0.035 0.002 TYR g 5 ARG 0.011 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2018 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1695 time to evaluate : 6.614 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: A 34 PHE cc_start: 0.7888 (t80) cc_final: 0.7631 (t80) REVERT: A 65 ASP cc_start: 0.8648 (t0) cc_final: 0.8317 (t0) REVERT: A 194 ASN cc_start: 0.8933 (t0) cc_final: 0.8563 (t0) REVERT: B 53 MET cc_start: 0.8378 (mtp) cc_final: 0.8049 (mtp) REVERT: B 97 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8153 (mtt180) REVERT: B 121 ASN cc_start: 0.8790 (t0) cc_final: 0.8300 (t0) REVERT: B 216 MET cc_start: 0.9100 (mmt) cc_final: 0.8445 (mmt) REVERT: B 309 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8259 (tt) REVERT: B 328 ASN cc_start: 0.7920 (m-40) cc_final: 0.7638 (m110) REVERT: C 13 GLU cc_start: 0.8417 (pp20) cc_final: 0.8097 (pp20) REVERT: C 94 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8187 (m110) REVERT: C 201 ARG cc_start: 0.8601 (mmm160) cc_final: 0.8347 (mmm-85) REVERT: C 335 MET cc_start: 0.8266 (ttm) cc_final: 0.8014 (ttm) REVERT: D 89 LYS cc_start: 0.7549 (tttt) cc_final: 0.7007 (tttm) REVERT: D 152 ARG cc_start: 0.8700 (tpt170) cc_final: 0.8354 (tpt170) REVERT: E 115 TYR cc_start: 0.8253 (t80) cc_final: 0.7935 (t80) REVERT: E 205 ASP cc_start: 0.8194 (p0) cc_final: 0.7748 (p0) REVERT: E 245 GLN cc_start: 0.7745 (tp40) cc_final: 0.7382 (tp40) REVERT: E 274 GLN cc_start: 0.8713 (mt0) cc_final: 0.8424 (mt0) REVERT: E 282 TYR cc_start: 0.8955 (m-80) cc_final: 0.8643 (m-80) REVERT: F 193 GLU cc_start: 0.8273 (tp30) cc_final: 0.7872 (tp30) REVERT: F 247 MET cc_start: 0.8927 (mmm) cc_final: 0.8357 (ttm) REVERT: G 74 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8647 (mm) REVERT: G 75 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8399 (mtpp) REVERT: G 167 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9162 (t) REVERT: G 192 HIS cc_start: 0.5809 (t-90) cc_final: 0.5600 (t-170) REVERT: G 211 ASP cc_start: 0.8490 (m-30) cc_final: 0.8072 (m-30) REVERT: G 228 ASP cc_start: 0.8368 (t0) cc_final: 0.8133 (t0) REVERT: H 8 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7323 (tm-30) REVERT: H 92 MET cc_start: 0.8228 (mtp) cc_final: 0.7875 (mtm) REVERT: I 57 TYR cc_start: 0.8983 (t80) cc_final: 0.8702 (t80) REVERT: I 170 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8747 (mmmm) REVERT: J 104 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: J 140 SER cc_start: 0.9432 (m) cc_final: 0.9114 (t) REVERT: J 168 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8409 (tm-30) REVERT: K 17 ASP cc_start: 0.8826 (t0) cc_final: 0.8122 (t0) REVERT: K 20 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8406 (mp10) REVERT: K 99 ASP cc_start: 0.9106 (t0) cc_final: 0.8716 (t0) REVERT: K 119 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8460 (tm-30) REVERT: K 157 ILE cc_start: 0.8495 (mm) cc_final: 0.8148 (mm) REVERT: K 201 GLU cc_start: 0.8320 (pp20) cc_final: 0.7903 (tm-30) REVERT: L 6 TYR cc_start: 0.8974 (m-80) cc_final: 0.8551 (m-80) REVERT: L 99 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: L 124 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7649 (mttp) REVERT: M 12 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8413 (mtt180) REVERT: M 145 ASN cc_start: 0.8792 (t0) cc_final: 0.8276 (t0) REVERT: N 96 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: N 100 GLU cc_start: 0.8622 (mp0) cc_final: 0.8109 (mp0) REVERT: N 169 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7875 (mtp180) REVERT: O 34 GLN cc_start: 0.8768 (tp40) cc_final: 0.8550 (tp40) REVERT: P 14 ARG cc_start: 0.8243 (ptt90) cc_final: 0.7953 (ptt90) REVERT: P 17 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: P 175 GLU cc_start: 0.8490 (mp0) cc_final: 0.8096 (mp0) REVERT: Q 91 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8543 (m90) REVERT: R 3 ASN cc_start: 0.8155 (t0) cc_final: 0.7907 (t0) REVERT: R 96 ILE cc_start: 0.9192 (mm) cc_final: 0.8952 (tt) REVERT: R 111 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7542 (tm-30) REVERT: S 30 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7646 (mt-10) REVERT: S 34 MET cc_start: 0.8133 (ppp) cc_final: 0.7223 (ppp) REVERT: S 44 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7931 (tm-30) REVERT: S 64 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6824 (tm-30) REVERT: S 108 GLU cc_start: 0.8086 (tt0) cc_final: 0.7687 (tp30) REVERT: T 35 LYS cc_start: 0.8389 (mmpt) cc_final: 0.7878 (mmtp) REVERT: T 112 MET cc_start: 0.8438 (mmm) cc_final: 0.8198 (mmm) REVERT: V 69 ASN cc_start: 0.9046 (t0) cc_final: 0.8611 (t0) REVERT: V 145 ASP cc_start: 0.8170 (t0) cc_final: 0.7888 (t70) REVERT: W 120 GLU cc_start: 0.7825 (pp20) cc_final: 0.7562 (pp20) REVERT: X 18 TYR cc_start: 0.8938 (m-80) cc_final: 0.8015 (m-80) REVERT: X 57 MET cc_start: 0.7805 (mtp) cc_final: 0.7433 (mtt) REVERT: X 97 ASN cc_start: 0.8887 (t0) cc_final: 0.8650 (p0) REVERT: X 113 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8754 (tp30) REVERT: Y 48 TYR cc_start: 0.8915 (m-80) cc_final: 0.8532 (m-80) REVERT: Y 61 TYR cc_start: 0.9115 (m-80) cc_final: 0.8400 (m-80) REVERT: Y 108 TYR cc_start: 0.9119 (m-80) cc_final: 0.8712 (m-80) REVERT: Y 120 GLN cc_start: 0.8473 (mt0) cc_final: 0.8237 (mt0) REVERT: Y 134 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7710 (tm-30) REVERT: Z 3 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: Z 11 ASN cc_start: 0.8298 (t0) cc_final: 0.7955 (t0) REVERT: a 29 LEU cc_start: 0.8973 (mt) cc_final: 0.8737 (mp) REVERT: a 57 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8659 (ttmt) REVERT: b 40 LYS cc_start: 0.8003 (mttm) cc_final: 0.7561 (mtmm) REVERT: b 79 ASN cc_start: 0.8469 (m-40) cc_final: 0.8181 (m110) REVERT: b 101 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7453 (mmtp) REVERT: b 109 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9220 (m) REVERT: c 52 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8756 (mm110) REVERT: c 70 LEU cc_start: 0.9060 (mp) cc_final: 0.8834 (mt) REVERT: c 86 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: d 31 GLU cc_start: 0.8288 (tt0) cc_final: 0.8053 (tm-30) REVERT: d 50 VAL cc_start: 0.9296 (t) cc_final: 0.8966 (p) REVERT: e 3 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8119 (tm-30) REVERT: e 28 ASN cc_start: 0.8280 (t0) cc_final: 0.8059 (t0) REVERT: e 100 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8143 (tp-100) REVERT: f 27 GLU cc_start: 0.8100 (tp30) cc_final: 0.7511 (tp30) REVERT: f 108 GLN cc_start: 0.8652 (mt0) cc_final: 0.8291 (mt0) REVERT: g 43 MET cc_start: 0.7767 (tmm) cc_final: 0.7356 (tmm) REVERT: i 16 ARG cc_start: 0.8908 (ptp90) cc_final: 0.8530 (ttm110) REVERT: i 58 GLN cc_start: 0.8017 (mp10) cc_final: 0.7739 (mp10) REVERT: j 15 LYS cc_start: 0.8677 (tttm) cc_final: 0.8275 (tttt) REVERT: k 114 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7912 (ptpt) REVERT: l 2 ARG cc_start: 0.8635 (ttt180) cc_final: 0.7649 (ttm170) REVERT: l 4 LYS cc_start: 0.8602 (tttt) cc_final: 0.6879 (mmtt) REVERT: l 10 MET cc_start: 0.8566 (tpp) cc_final: 0.8320 (tpp) REVERT: l 15 ARG cc_start: 0.8364 (ptt180) cc_final: 0.7869 (mtt-85) REVERT: l 21 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.6848 (tpt170) REVERT: m 59 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8425 (mptt) REVERT: n 6 LYS cc_start: 0.8647 (tptt) cc_final: 0.8145 (tptt) REVERT: n 28 LYS cc_start: 0.8701 (tttp) cc_final: 0.8487 (ttpp) REVERT: n 83 ILE cc_start: 0.9187 (mt) cc_final: 0.8934 (mt) REVERT: o 7 GLN cc_start: 0.9033 (mp10) cc_final: 0.8689 (mp10) REVERT: o 25 ASP cc_start: 0.8184 (t70) cc_final: 0.7667 (t70) REVERT: o 86 ASN cc_start: 0.9178 (t0) cc_final: 0.8872 (t0) REVERT: o 104 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8258 (ptp90) REVERT: o 162 ARG cc_start: 0.6357 (ttm170) cc_final: 0.5901 (tmt170) REVERT: p 64 MET cc_start: 0.8521 (mtp) cc_final: 0.8161 (mtp) REVERT: p 70 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7286 (mm-40) REVERT: t 55 MET cc_start: 0.8006 (ttm) cc_final: 0.7637 (ttp) REVERT: t 175 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7923 (m90) REVERT: t 182 ILE cc_start: 0.8599 (mm) cc_final: 0.8204 (mp) REVERT: t 271 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8596 (ttp-110) outliers start: 323 outliers final: 228 residues processed: 1845 average time/residue: 1.2258 time to fit residues: 3918.3260 Evaluate side-chains 1877 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1633 time to evaluate : 6.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 91 HIS Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain d residue 56 ASN Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 9 LYS Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 60 CYS Chi-restraints excluded: chain n residue 73 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 171 ASN Chi-restraints excluded: chain t residue 175 HIS Chi-restraints excluded: chain t residue 219 GLU Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 837 optimal weight: 10.0000 chunk 570 optimal weight: 0.0670 chunk 14 optimal weight: 5.9990 chunk 748 optimal weight: 10.0000 chunk 414 optimal weight: 0.8980 chunk 857 optimal weight: 10.0000 chunk 694 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 513 optimal weight: 0.9990 chunk 902 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 204 GLN B 258 HIS ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN C 347 HIS ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN E 256 GLN F 63 GLN F 206 ASN G 43 GLN H 63 ASN I 14 ASN I 123 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 GLN M 37 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN O 10 ASN S 94 ASN S 105 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN Y 66 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 ASN m 19 GLN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN ** t 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 148782 Z= 0.181 Angle : 0.510 15.344 219691 Z= 0.259 Chirality : 0.032 0.255 27408 Planarity : 0.004 0.079 13321 Dihedral : 23.515 179.843 69312 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.14 % Allowed : 21.52 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 6651 helix: 1.00 (0.11), residues: 2177 sheet: -0.93 (0.16), residues: 928 loop : -0.97 (0.10), residues: 3546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 266 HIS 0.007 0.001 HIS Y 40 PHE 0.017 0.001 PHE B 102 TYR 0.027 0.001 TYR H 96 ARG 0.011 0.000 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1992 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1694 time to evaluate : 6.550 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: A 65 ASP cc_start: 0.8634 (t0) cc_final: 0.8277 (t0) REVERT: A 95 GLN cc_start: 0.8322 (mp-120) cc_final: 0.7778 (mp10) REVERT: A 194 ASN cc_start: 0.8948 (t0) cc_final: 0.8528 (t0) REVERT: B 53 MET cc_start: 0.8394 (mtp) cc_final: 0.8080 (mtp) REVERT: B 97 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8154 (mtt180) REVERT: B 121 ASN cc_start: 0.8836 (t0) cc_final: 0.8351 (t0) REVERT: B 216 MET cc_start: 0.9031 (mmt) cc_final: 0.8234 (mmt) REVERT: B 309 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8262 (tt) REVERT: B 328 ASN cc_start: 0.7840 (m-40) cc_final: 0.7580 (m110) REVERT: C 13 GLU cc_start: 0.8422 (pp20) cc_final: 0.8088 (pp20) REVERT: C 92 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8702 (p90) REVERT: C 94 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8136 (m110) REVERT: C 101 MET cc_start: 0.8764 (ptm) cc_final: 0.8422 (ptm) REVERT: C 201 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8351 (mmm-85) REVERT: C 293 LEU cc_start: 0.9527 (mt) cc_final: 0.9313 (mt) REVERT: C 335 MET cc_start: 0.8327 (ttm) cc_final: 0.8083 (ttm) REVERT: D 89 LYS cc_start: 0.7513 (tttt) cc_final: 0.7304 (tttt) REVERT: D 152 ARG cc_start: 0.8673 (tpt170) cc_final: 0.8349 (tpt170) REVERT: E 115 TYR cc_start: 0.7957 (t80) cc_final: 0.7665 (t80) REVERT: E 205 ASP cc_start: 0.8192 (p0) cc_final: 0.7626 (p0) REVERT: E 245 GLN cc_start: 0.7749 (tp40) cc_final: 0.7510 (tp40) REVERT: E 274 GLN cc_start: 0.8687 (mt0) cc_final: 0.8403 (mt0) REVERT: E 282 TYR cc_start: 0.8934 (m-80) cc_final: 0.8630 (m-80) REVERT: F 110 GLN cc_start: 0.9000 (mt0) cc_final: 0.8778 (mt0) REVERT: F 193 GLU cc_start: 0.8236 (tp30) cc_final: 0.7841 (tp30) REVERT: F 247 MET cc_start: 0.8932 (mmm) cc_final: 0.8401 (ttm) REVERT: G 74 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8613 (mm) REVERT: G 75 LYS cc_start: 0.8654 (mtmt) cc_final: 0.7932 (mtpp) REVERT: G 167 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9086 (t) REVERT: G 192 HIS cc_start: 0.5793 (t-90) cc_final: 0.5542 (t-170) REVERT: G 211 ASP cc_start: 0.8491 (m-30) cc_final: 0.8048 (m-30) REVERT: G 228 ASP cc_start: 0.8349 (t0) cc_final: 0.8101 (t0) REVERT: G 240 ASN cc_start: 0.9018 (t0) cc_final: 0.8498 (t0) REVERT: H 8 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7337 (tm-30) REVERT: H 42 ASN cc_start: 0.8246 (t0) cc_final: 0.8005 (t0) REVERT: H 66 GLU cc_start: 0.7838 (mp0) cc_final: 0.7169 (mp0) REVERT: H 92 MET cc_start: 0.8212 (mtp) cc_final: 0.7822 (mtm) REVERT: H 175 PHE cc_start: 0.8741 (m-80) cc_final: 0.8190 (m-80) REVERT: I 11 TYR cc_start: 0.8140 (m-80) cc_final: 0.7756 (m-10) REVERT: I 57 TYR cc_start: 0.8957 (t80) cc_final: 0.8725 (t80) REVERT: J 92 TYR cc_start: 0.8589 (m-10) cc_final: 0.8275 (m-10) REVERT: J 98 ASN cc_start: 0.8824 (m110) cc_final: 0.8325 (m110) REVERT: J 140 SER cc_start: 0.9391 (m) cc_final: 0.9047 (t) REVERT: J 168 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8360 (tm-30) REVERT: K 17 ASP cc_start: 0.8805 (t0) cc_final: 0.7981 (t0) REVERT: K 20 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8406 (mp10) REVERT: K 99 ASP cc_start: 0.9095 (t0) cc_final: 0.8702 (t0) REVERT: L 6 TYR cc_start: 0.8976 (m-80) cc_final: 0.8610 (m-80) REVERT: L 99 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: L 124 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7738 (mttp) REVERT: M 12 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8365 (mtt180) REVERT: M 145 ASN cc_start: 0.8717 (t0) cc_final: 0.8160 (t0) REVERT: N 96 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: N 100 GLU cc_start: 0.8628 (mp0) cc_final: 0.8143 (mp0) REVERT: N 169 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7874 (mtp180) REVERT: O 34 GLN cc_start: 0.8771 (tp40) cc_final: 0.8569 (tp40) REVERT: P 14 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7945 (ptt90) REVERT: P 17 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: P 175 GLU cc_start: 0.8543 (mp0) cc_final: 0.8198 (mp0) REVERT: R 111 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7512 (tm-30) REVERT: S 30 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7636 (mt-10) REVERT: S 34 MET cc_start: 0.8195 (ppp) cc_final: 0.7105 (ppp) REVERT: S 44 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8058 (tm-30) REVERT: S 64 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6850 (tm-30) REVERT: S 81 ARG cc_start: 0.8372 (mmt90) cc_final: 0.7959 (mmt90) REVERT: S 108 GLU cc_start: 0.8132 (tt0) cc_final: 0.7694 (tp30) REVERT: T 35 LYS cc_start: 0.8477 (mmpt) cc_final: 0.7986 (mmtp) REVERT: T 112 MET cc_start: 0.8428 (mmm) cc_final: 0.8208 (mmm) REVERT: V 69 ASN cc_start: 0.9020 (t0) cc_final: 0.8637 (t0) REVERT: V 145 ASP cc_start: 0.8108 (t0) cc_final: 0.7872 (t70) REVERT: W 120 GLU cc_start: 0.7919 (pp20) cc_final: 0.7661 (pp20) REVERT: X 18 TYR cc_start: 0.8964 (m-80) cc_final: 0.8464 (m-80) REVERT: X 57 MET cc_start: 0.7730 (mtp) cc_final: 0.7369 (mtt) REVERT: X 113 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8778 (tp30) REVERT: Y 44 ASN cc_start: 0.9127 (t0) cc_final: 0.8881 (t0) REVERT: Y 48 TYR cc_start: 0.8894 (m-80) cc_final: 0.8458 (m-80) REVERT: Y 61 TYR cc_start: 0.9089 (m-80) cc_final: 0.8363 (m-80) REVERT: Y 87 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8340 (ttp80) REVERT: Y 108 TYR cc_start: 0.9088 (m-80) cc_final: 0.8457 (m-80) REVERT: Y 120 GLN cc_start: 0.8506 (mt0) cc_final: 0.8124 (mt0) REVERT: Z 3 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8605 (mtmm) REVERT: Z 28 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7693 (ttm170) REVERT: a 29 LEU cc_start: 0.8957 (mt) cc_final: 0.8747 (mp) REVERT: a 57 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8628 (ttmt) REVERT: b 40 LYS cc_start: 0.7933 (mttm) cc_final: 0.7507 (mtmm) REVERT: b 79 ASN cc_start: 0.8393 (m-40) cc_final: 0.8087 (m110) REVERT: b 109 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9207 (m) REVERT: c 52 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8737 (mm110) REVERT: c 57 ASN cc_start: 0.9200 (p0) cc_final: 0.8995 (p0) REVERT: c 70 LEU cc_start: 0.9046 (mp) cc_final: 0.8814 (mt) REVERT: d 25 THR cc_start: 0.9022 (m) cc_final: 0.8776 (m) REVERT: d 31 GLU cc_start: 0.8255 (tt0) cc_final: 0.8017 (tm-30) REVERT: d 50 VAL cc_start: 0.9282 (t) cc_final: 0.8930 (p) REVERT: e 3 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8164 (tm-30) REVERT: e 28 ASN cc_start: 0.8267 (t0) cc_final: 0.8037 (t0) REVERT: e 66 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8153 (mtt180) REVERT: e 100 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8386 (tp-100) REVERT: f 27 GLU cc_start: 0.8099 (tp30) cc_final: 0.7492 (tp30) REVERT: f 108 GLN cc_start: 0.8633 (mt0) cc_final: 0.8270 (mt0) REVERT: g 43 MET cc_start: 0.7751 (tmm) cc_final: 0.7217 (tmm) REVERT: i 16 ARG cc_start: 0.8900 (ptp90) cc_final: 0.8523 (ttm110) REVERT: i 58 GLN cc_start: 0.7914 (mp10) cc_final: 0.7702 (mp10) REVERT: j 15 LYS cc_start: 0.8680 (tttm) cc_final: 0.8192 (tttp) REVERT: k 114 LYS cc_start: 0.8125 (ptmt) cc_final: 0.7811 (ptpt) REVERT: l 2 ARG cc_start: 0.8552 (ttt180) cc_final: 0.7579 (ttm170) REVERT: l 4 LYS cc_start: 0.8568 (tttt) cc_final: 0.6839 (mmtt) REVERT: l 10 MET cc_start: 0.8615 (tpp) cc_final: 0.8386 (tpp) REVERT: l 15 ARG cc_start: 0.8323 (ptt180) cc_final: 0.7879 (mtt-85) REVERT: l 21 ARG cc_start: 0.8415 (tpt-90) cc_final: 0.6683 (tpt170) REVERT: m 59 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8423 (mptt) REVERT: n 6 LYS cc_start: 0.8591 (tptt) cc_final: 0.8052 (tptp) REVERT: n 27 LYS cc_start: 0.8994 (tttt) cc_final: 0.8726 (ttmt) REVERT: n 28 LYS cc_start: 0.8652 (tttp) cc_final: 0.8381 (ttpp) REVERT: n 83 ILE cc_start: 0.9179 (mt) cc_final: 0.8925 (mt) REVERT: o 7 GLN cc_start: 0.9006 (mp10) cc_final: 0.8682 (mp10) REVERT: o 86 ASN cc_start: 0.9069 (t0) cc_final: 0.8845 (t0) REVERT: o 162 ARG cc_start: 0.6387 (ttm170) cc_final: 0.5938 (tmt170) REVERT: p 48 THR cc_start: 0.9043 (m) cc_final: 0.8779 (p) REVERT: p 64 MET cc_start: 0.8509 (mtp) cc_final: 0.8118 (mtp) REVERT: p 84 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8434 (mmtt) REVERT: t 55 MET cc_start: 0.8154 (ttm) cc_final: 0.7689 (ttp) REVERT: t 175 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7925 (m90) REVERT: t 219 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: t 271 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8800 (ptm-80) outliers start: 298 outliers final: 235 residues processed: 1819 average time/residue: 1.2097 time to fit residues: 3810.0241 Evaluate side-chains 1867 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1617 time to evaluate : 6.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 56 GLN Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 90 ILE Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 56 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 66 ARG Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 9 LYS Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 60 CYS Chi-restraints excluded: chain n residue 73 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 175 HIS Chi-restraints excluded: chain t residue 219 GLU Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 338 optimal weight: 6.9990 chunk 905 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 590 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 1006 optimal weight: 10.0000 chunk 835 optimal weight: 9.9990 chunk 465 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 528 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 158 GLN B 167 GLN B 204 GLN B 258 HIS ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 206 ASN G 85 GLN H 78 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 37 HIS N 14 HIS N 26 GLN S 105 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN b 34 HIS b 121 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 HIS g 92 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN t 8 GLN t 96 GLN t 134 GLN ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 242 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 148782 Z= 0.257 Angle : 0.545 15.245 219691 Z= 0.276 Chirality : 0.033 0.268 27408 Planarity : 0.004 0.086 13321 Dihedral : 23.499 179.559 69312 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.05 % Allowed : 21.61 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6651 helix: 1.01 (0.11), residues: 2202 sheet: -0.89 (0.16), residues: 930 loop : -0.92 (0.11), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 266 HIS 0.025 0.001 HIS B 258 PHE 0.017 0.001 PHE I 159 TYR 0.031 0.002 TYR M 30 ARG 0.011 0.001 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1997 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1646 time to evaluate : 6.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.7910 (t80) cc_final: 0.7645 (t80) REVERT: A 65 ASP cc_start: 0.8657 (t0) cc_final: 0.8313 (t0) REVERT: A 95 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: A 194 ASN cc_start: 0.8939 (t0) cc_final: 0.8493 (t0) REVERT: B 53 MET cc_start: 0.8349 (mtp) cc_final: 0.8076 (mtp) REVERT: B 74 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: B 97 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8201 (mtt180) REVERT: B 121 ASN cc_start: 0.8789 (t0) cc_final: 0.8286 (t0) REVERT: B 309 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 328 ASN cc_start: 0.7852 (m-40) cc_final: 0.7600 (m110) REVERT: B 332 MET cc_start: 0.7524 (ttt) cc_final: 0.7027 (ttt) REVERT: C 13 GLU cc_start: 0.8471 (pp20) cc_final: 0.8139 (pp20) REVERT: C 94 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8145 (m110) REVERT: C 101 MET cc_start: 0.8746 (ptm) cc_final: 0.8383 (ptm) REVERT: C 187 GLN cc_start: 0.9014 (pt0) cc_final: 0.8802 (pt0) REVERT: C 201 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8357 (mmm-85) REVERT: D 34 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8331 (tttm) REVERT: D 152 ARG cc_start: 0.8699 (tpt170) cc_final: 0.8353 (tpt170) REVERT: D 236 MET cc_start: 0.8127 (mtp) cc_final: 0.7757 (ptm) REVERT: E 115 TYR cc_start: 0.7996 (t80) cc_final: 0.7601 (t80) REVERT: E 205 ASP cc_start: 0.8234 (p0) cc_final: 0.7809 (p0) REVERT: E 207 LYS cc_start: 0.8898 (tptt) cc_final: 0.8576 (tppt) REVERT: E 245 GLN cc_start: 0.7869 (tp40) cc_final: 0.7581 (tp40) REVERT: E 274 GLN cc_start: 0.8697 (mt0) cc_final: 0.8420 (mt0) REVERT: E 282 TYR cc_start: 0.8939 (m-80) cc_final: 0.8638 (m-80) REVERT: F 193 GLU cc_start: 0.8275 (tp30) cc_final: 0.7875 (tp30) REVERT: F 247 MET cc_start: 0.8914 (mmm) cc_final: 0.8357 (ttm) REVERT: G 74 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (mm) REVERT: G 75 LYS cc_start: 0.8665 (mtmt) cc_final: 0.7885 (mtpp) REVERT: G 167 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9162 (t) REVERT: G 192 HIS cc_start: 0.5828 (t-90) cc_final: 0.5572 (t-170) REVERT: G 211 ASP cc_start: 0.8552 (m-30) cc_final: 0.8119 (m-30) REVERT: G 228 ASP cc_start: 0.8352 (t0) cc_final: 0.8107 (t0) REVERT: G 240 ASN cc_start: 0.9026 (t0) cc_final: 0.8494 (t0) REVERT: H 8 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7324 (tm-30) REVERT: H 92 MET cc_start: 0.8302 (mtp) cc_final: 0.8002 (mtm) REVERT: H 172 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8348 (mp) REVERT: I 57 TYR cc_start: 0.8970 (t80) cc_final: 0.8688 (t80) REVERT: J 140 SER cc_start: 0.9413 (m) cc_final: 0.9078 (t) REVERT: J 168 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8397 (tm-30) REVERT: K 99 ASP cc_start: 0.9120 (t0) cc_final: 0.8745 (t0) REVERT: K 158 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7155 (ttm170) REVERT: L 6 TYR cc_start: 0.9011 (m-80) cc_final: 0.8612 (m-80) REVERT: L 99 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: L 104 MET cc_start: 0.8933 (ttm) cc_final: 0.8500 (ttp) REVERT: L 124 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7794 (mttp) REVERT: M 12 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8384 (mtt180) REVERT: M 30 TYR cc_start: 0.8700 (m-80) cc_final: 0.8354 (m-80) REVERT: M 68 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8476 (ttm170) REVERT: M 145 ASN cc_start: 0.8737 (t0) cc_final: 0.8164 (t0) REVERT: N 96 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: N 100 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: N 169 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7841 (mtp180) REVERT: O 34 GLN cc_start: 0.8806 (tp40) cc_final: 0.8564 (tp40) REVERT: O 49 LYS cc_start: 0.8772 (mttm) cc_final: 0.8464 (mmmt) REVERT: P 6 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7251 (ptm-80) REVERT: P 14 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7949 (ptt90) REVERT: P 17 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: P 168 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8537 (ttp80) REVERT: P 175 GLU cc_start: 0.8502 (mp0) cc_final: 0.8142 (mp0) REVERT: R 3 ASN cc_start: 0.8089 (t0) cc_final: 0.7885 (t0) REVERT: R 111 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7557 (tm-30) REVERT: S 30 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7643 (mt-10) REVERT: S 34 MET cc_start: 0.8200 (ppp) cc_final: 0.7973 (ppp) REVERT: S 64 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6743 (tm-30) REVERT: S 108 GLU cc_start: 0.8147 (tt0) cc_final: 0.7588 (tp30) REVERT: T 35 LYS cc_start: 0.8450 (mmpt) cc_final: 0.7957 (mmtp) REVERT: T 112 MET cc_start: 0.8440 (mmm) cc_final: 0.8176 (mmm) REVERT: V 69 ASN cc_start: 0.9017 (t0) cc_final: 0.8657 (t0) REVERT: V 145 ASP cc_start: 0.8237 (t0) cc_final: 0.8007 (t70) REVERT: W 120 GLU cc_start: 0.7956 (pp20) cc_final: 0.7695 (pp20) REVERT: X 18 TYR cc_start: 0.8936 (m-80) cc_final: 0.8505 (m-80) REVERT: X 57 MET cc_start: 0.7745 (mtp) cc_final: 0.7338 (mtt) REVERT: X 113 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8804 (tp30) REVERT: Y 44 ASN cc_start: 0.9141 (t0) cc_final: 0.8881 (t0) REVERT: Y 48 TYR cc_start: 0.8892 (m-80) cc_final: 0.8377 (m-80) REVERT: Y 61 TYR cc_start: 0.9116 (m-80) cc_final: 0.8395 (m-80) REVERT: Y 108 TYR cc_start: 0.9104 (m-80) cc_final: 0.8619 (m-80) REVERT: Y 120 GLN cc_start: 0.8518 (mt0) cc_final: 0.8185 (mt0) REVERT: Z 3 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8594 (mtmm) REVERT: Z 11 ASN cc_start: 0.8309 (t0) cc_final: 0.7968 (t0) REVERT: Z 28 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7653 (ttm170) REVERT: a 29 LEU cc_start: 0.8985 (mt) cc_final: 0.8766 (mp) REVERT: a 57 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8652 (ttmt) REVERT: b 40 LYS cc_start: 0.7991 (mttm) cc_final: 0.7569 (mtmm) REVERT: b 79 ASN cc_start: 0.8490 (m-40) cc_final: 0.8081 (m-40) REVERT: b 96 GLU cc_start: 0.8107 (pm20) cc_final: 0.7906 (pm20) REVERT: c 52 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8765 (mm110) REVERT: c 70 LEU cc_start: 0.9062 (mp) cc_final: 0.8837 (mt) REVERT: c 86 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: d 31 GLU cc_start: 0.8275 (tt0) cc_final: 0.8006 (tm-30) REVERT: d 50 VAL cc_start: 0.9280 (t) cc_final: 0.8954 (p) REVERT: e 3 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8151 (tm-30) REVERT: e 100 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8402 (tp-100) REVERT: f 27 GLU cc_start: 0.8069 (tp30) cc_final: 0.7476 (tp30) REVERT: f 87 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7818 (ptpp) REVERT: f 108 GLN cc_start: 0.8611 (mt0) cc_final: 0.8281 (mt0) REVERT: g 43 MET cc_start: 0.7809 (tmm) cc_final: 0.7212 (tmm) REVERT: i 3 ARG cc_start: 0.8560 (mmt180) cc_final: 0.8339 (mmt180) REVERT: i 16 ARG cc_start: 0.8920 (ptp90) cc_final: 0.8527 (ttm110) REVERT: j 15 LYS cc_start: 0.8714 (tttm) cc_final: 0.8213 (tttp) REVERT: j 36 ARG cc_start: 0.7012 (mtt180) cc_final: 0.6733 (mtt180) REVERT: k 114 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7828 (ptpt) REVERT: l 2 ARG cc_start: 0.8617 (ttt180) cc_final: 0.7565 (ttm170) REVERT: l 4 LYS cc_start: 0.8582 (tttt) cc_final: 0.6845 (mmtt) REVERT: l 15 ARG cc_start: 0.8345 (ptt180) cc_final: 0.7888 (mtt-85) REVERT: l 21 ARG cc_start: 0.8423 (tpt-90) cc_final: 0.6670 (tpt170) REVERT: n 6 LYS cc_start: 0.8589 (tptt) cc_final: 0.8082 (tptp) REVERT: n 28 LYS cc_start: 0.8696 (tttp) cc_final: 0.8481 (ttpp) REVERT: n 83 ILE cc_start: 0.9189 (mt) cc_final: 0.8936 (mt) REVERT: o 7 GLN cc_start: 0.9012 (mp10) cc_final: 0.8694 (mp10) REVERT: o 86 ASN cc_start: 0.9136 (t0) cc_final: 0.8853 (t0) REVERT: o 104 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8195 (ptp90) REVERT: o 162 ARG cc_start: 0.6312 (ttm170) cc_final: 0.5836 (tmt170) REVERT: p 48 THR cc_start: 0.9045 (m) cc_final: 0.8787 (p) REVERT: p 64 MET cc_start: 0.8522 (mtp) cc_final: 0.8134 (mtp) REVERT: t 55 MET cc_start: 0.8320 (ttm) cc_final: 0.8110 (ttm) REVERT: t 88 HIS cc_start: 0.8662 (m170) cc_final: 0.8348 (m-70) REVERT: t 96 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5654 (pp30) REVERT: t 175 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7932 (m90) REVERT: t 219 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: t 271 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8924 (ttp-110) outliers start: 351 outliers final: 281 residues processed: 1815 average time/residue: 1.2223 time to fit residues: 3847.4692 Evaluate side-chains 1915 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1612 time to evaluate : 6.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 68 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 100 GLU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 56 GLN Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 82 VAL Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 56 ASN Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 20 THR Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 90 LEU Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 9 LYS Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 73 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 96 GLN Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 135 VAL Chi-restraints excluded: chain t residue 164 THR Chi-restraints excluded: chain t residue 171 ASN Chi-restraints excluded: chain t residue 175 HIS Chi-restraints excluded: chain t residue 219 GLU Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 970 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 573 optimal weight: 5.9990 chunk 734 optimal weight: 8.9990 chunk 569 optimal weight: 10.0000 chunk 847 optimal weight: 10.0000 chunk 561 optimal weight: 1.9990 chunk 1002 optimal weight: 8.9990 chunk 627 optimal weight: 8.9990 chunk 611 optimal weight: 6.9990 chunk 462 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN H 76 HIS H 78 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS N 26 GLN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN Y 66 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 GLN e 112 GLN g 92 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN t 8 GLN ** t 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 148782 Z= 0.379 Angle : 0.643 15.680 219691 Z= 0.325 Chirality : 0.038 0.289 27408 Planarity : 0.005 0.093 13321 Dihedral : 23.592 179.795 69312 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.80 % Favored : 94.18 % Rotamer: Outliers : 6.41 % Allowed : 21.88 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 6651 helix: 0.83 (0.11), residues: 2224 sheet: -0.98 (0.16), residues: 935 loop : -0.97 (0.11), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 266 HIS 0.012 0.001 HIS t 299 PHE 0.018 0.002 PHE I 159 TYR 0.029 0.002 TYR M 30 ARG 0.009 0.001 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2019 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1647 time to evaluate : 8.387 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: A 65 ASP cc_start: 0.8718 (t0) cc_final: 0.8396 (t0) REVERT: A 95 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7722 (mp-120) REVERT: A 194 ASN cc_start: 0.8986 (t0) cc_final: 0.8568 (t0) REVERT: B 53 MET cc_start: 0.8360 (mtp) cc_final: 0.8156 (mtp) REVERT: B 74 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: B 97 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8270 (mtt180) REVERT: B 121 ASN cc_start: 0.8770 (t0) cc_final: 0.8307 (t0) REVERT: B 279 GLU cc_start: 0.6153 (tm-30) cc_final: 0.5942 (tm-30) REVERT: B 309 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 328 ASN cc_start: 0.7905 (m-40) cc_final: 0.7596 (m110) REVERT: B 332 MET cc_start: 0.7596 (ttt) cc_final: 0.7070 (ttt) REVERT: C 92 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8835 (p90) REVERT: C 94 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8435 (m110) REVERT: C 101 MET cc_start: 0.8632 (ptm) cc_final: 0.8347 (ptm) REVERT: C 201 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8294 (mmm-85) REVERT: D 34 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8419 (tttm) REVERT: D 152 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8332 (tpt170) REVERT: E 115 TYR cc_start: 0.8043 (t80) cc_final: 0.7683 (t80) REVERT: E 205 ASP cc_start: 0.8266 (p0) cc_final: 0.7845 (p0) REVERT: E 207 LYS cc_start: 0.8815 (tptt) cc_final: 0.8454 (tppt) REVERT: E 274 GLN cc_start: 0.8708 (mt0) cc_final: 0.8456 (mt0) REVERT: E 282 TYR cc_start: 0.8972 (m-80) cc_final: 0.8659 (m-80) REVERT: F 193 GLU cc_start: 0.8328 (tp30) cc_final: 0.7942 (tp30) REVERT: F 247 MET cc_start: 0.8893 (mmm) cc_final: 0.8219 (ttm) REVERT: G 74 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (mm) REVERT: G 75 LYS cc_start: 0.8688 (mtmt) cc_final: 0.7938 (mtpp) REVERT: G 148 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7156 (tm-30) REVERT: G 167 VAL cc_start: 0.9545 (OUTLIER) cc_final: 0.9283 (t) REVERT: G 192 HIS cc_start: 0.5892 (t-90) cc_final: 0.5630 (t-170) REVERT: G 199 CYS cc_start: 0.8647 (t) cc_final: 0.8314 (t) REVERT: G 211 ASP cc_start: 0.8556 (m-30) cc_final: 0.8122 (m-30) REVERT: G 228 ASP cc_start: 0.8371 (t0) cc_final: 0.8143 (t0) REVERT: G 240 ASN cc_start: 0.9025 (t0) cc_final: 0.8518 (t0) REVERT: H 8 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7352 (tm-30) REVERT: H 92 MET cc_start: 0.8331 (mtp) cc_final: 0.8033 (mtm) REVERT: J 41 GLU cc_start: 0.8390 (tp30) cc_final: 0.7601 (tp30) REVERT: J 92 TYR cc_start: 0.8567 (m-10) cc_final: 0.8199 (m-10) REVERT: J 140 SER cc_start: 0.9454 (m) cc_final: 0.9140 (t) REVERT: J 168 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8288 (tm-30) REVERT: K 99 ASP cc_start: 0.9148 (t0) cc_final: 0.8825 (t0) REVERT: K 158 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7185 (ttm170) REVERT: L 6 TYR cc_start: 0.9069 (m-80) cc_final: 0.8642 (m-80) REVERT: L 104 MET cc_start: 0.9019 (ttm) cc_final: 0.8620 (ttp) REVERT: M 12 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8509 (mtt180) REVERT: M 68 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7595 (ttm170) REVERT: M 145 ASN cc_start: 0.8824 (t0) cc_final: 0.8279 (t0) REVERT: N 81 TRP cc_start: 0.9244 (t60) cc_final: 0.9015 (t60) REVERT: N 96 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: N 100 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: N 169 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7836 (mtp180) REVERT: N 182 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7686 (mt-10) REVERT: O 34 GLN cc_start: 0.8818 (tp40) cc_final: 0.8511 (tp40) REVERT: O 49 LYS cc_start: 0.8790 (mttm) cc_final: 0.8494 (mmmt) REVERT: P 6 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7266 (ptm-80) REVERT: P 17 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: P 77 ASN cc_start: 0.8128 (t0) cc_final: 0.7818 (t0) REVERT: P 175 GLU cc_start: 0.8462 (mp0) cc_final: 0.8119 (mp0) REVERT: R 8 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7939 (ttm170) REVERT: R 111 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7506 (tm-30) REVERT: S 34 MET cc_start: 0.8190 (ppp) cc_final: 0.7892 (ppp) REVERT: S 64 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6757 (tm-30) REVERT: S 108 GLU cc_start: 0.8180 (tt0) cc_final: 0.7646 (tp30) REVERT: T 112 MET cc_start: 0.8489 (mmm) cc_final: 0.8214 (mmm) REVERT: V 63 LYS cc_start: 0.8896 (mptt) cc_final: 0.8682 (mptt) REVERT: V 69 ASN cc_start: 0.8973 (t0) cc_final: 0.8552 (t0) REVERT: W 10 ASP cc_start: 0.8859 (t0) cc_final: 0.8248 (t70) REVERT: W 69 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7882 (tptt) REVERT: W 120 GLU cc_start: 0.7918 (pp20) cc_final: 0.7634 (pp20) REVERT: X 18 TYR cc_start: 0.9002 (m-80) cc_final: 0.8257 (m-80) REVERT: X 80 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8657 (pp) REVERT: X 113 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8813 (tp30) REVERT: Y 44 ASN cc_start: 0.9165 (t0) cc_final: 0.8951 (t0) REVERT: Y 61 TYR cc_start: 0.9180 (m-80) cc_final: 0.8548 (m-80) REVERT: Y 108 TYR cc_start: 0.9137 (m-80) cc_final: 0.8699 (m-80) REVERT: Y 120 GLN cc_start: 0.8705 (mt0) cc_final: 0.8371 (mt0) REVERT: Z 3 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8539 (mtmm) REVERT: Z 11 ASN cc_start: 0.8359 (t0) cc_final: 0.8005 (t0) REVERT: a 57 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8708 (ttmt) REVERT: b 40 LYS cc_start: 0.8093 (mttm) cc_final: 0.7676 (mtmm) REVERT: b 79 ASN cc_start: 0.8613 (m-40) cc_final: 0.8210 (m-40) REVERT: c 52 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8827 (mm-40) REVERT: c 70 LEU cc_start: 0.9072 (mp) cc_final: 0.8844 (mt) REVERT: c 86 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: d 31 GLU cc_start: 0.8312 (tt0) cc_final: 0.8017 (tm-30) REVERT: d 38 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8002 (mt-10) REVERT: d 50 VAL cc_start: 0.9342 (t) cc_final: 0.9087 (p) REVERT: d 89 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7607 (mtp85) REVERT: e 100 GLN cc_start: 0.8706 (tp40) cc_final: 0.8187 (tp-100) REVERT: f 27 GLU cc_start: 0.8140 (tp30) cc_final: 0.7537 (tp30) REVERT: f 87 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (ptpp) REVERT: f 108 GLN cc_start: 0.8640 (mt0) cc_final: 0.8320 (mt0) REVERT: g 15 HIS cc_start: 0.8470 (t-170) cc_final: 0.8182 (t-170) REVERT: g 43 MET cc_start: 0.8137 (tmm) cc_final: 0.7642 (tmm) REVERT: i 3 ARG cc_start: 0.8518 (mmt180) cc_final: 0.8257 (mmt180) REVERT: j 15 LYS cc_start: 0.8658 (tttm) cc_final: 0.8159 (tttp) REVERT: j 36 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6938 (mtt180) REVERT: k 114 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7944 (ptpt) REVERT: l 2 ARG cc_start: 0.8637 (ttt180) cc_final: 0.7619 (ttm170) REVERT: l 4 LYS cc_start: 0.8624 (tttt) cc_final: 0.6642 (mmtt) REVERT: l 10 MET cc_start: 0.8598 (tpp) cc_final: 0.8354 (tpp) REVERT: l 15 ARG cc_start: 0.8349 (ptt180) cc_final: 0.7829 (mtt-85) REVERT: l 21 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.6709 (tpt170) REVERT: n 6 LYS cc_start: 0.8542 (tptt) cc_final: 0.7945 (tptt) REVERT: n 83 ILE cc_start: 0.9213 (mt) cc_final: 0.8963 (mt) REVERT: o 86 ASN cc_start: 0.9153 (t0) cc_final: 0.8778 (t0) REVERT: o 104 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7998 (ptp90) REVERT: o 162 ARG cc_start: 0.6507 (ttm170) cc_final: 0.5999 (tmt170) REVERT: p 28 GLU cc_start: 0.7810 (mp0) cc_final: 0.7252 (mp0) REVERT: p 48 THR cc_start: 0.9060 (m) cc_final: 0.8798 (p) REVERT: p 58 LYS cc_start: 0.8750 (pttt) cc_final: 0.8371 (ptpt) REVERT: p 64 MET cc_start: 0.8539 (mtp) cc_final: 0.8219 (mtp) REVERT: p 71 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7418 (ptt90) REVERT: t 55 MET cc_start: 0.8281 (ttm) cc_final: 0.8045 (ttm) REVERT: t 183 GLU cc_start: 0.7924 (mp0) cc_final: 0.7698 (mp0) REVERT: t 219 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: t 271 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8937 (ttp-110) REVERT: t 326 MET cc_start: 0.5585 (mmm) cc_final: 0.5373 (mmm) outliers start: 372 outliers final: 302 residues processed: 1831 average time/residue: 1.2059 time to fit residues: 3832.7659 Evaluate side-chains 1923 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1599 time to evaluate : 6.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 68 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 100 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 56 GLN Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 ILE Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 69 LYS Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 82 VAL Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 102 ASN Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 91 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 67 LEU Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 9 LYS Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 96 CYS Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain l residue 9 ARG Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 135 VAL Chi-restraints excluded: chain t residue 164 THR Chi-restraints excluded: chain t residue 171 ASN Chi-restraints excluded: chain t residue 219 GLU Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 620 optimal weight: 8.9990 chunk 400 optimal weight: 3.9990 chunk 598 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 637 optimal weight: 10.0000 chunk 682 optimal weight: 20.0000 chunk 495 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 787 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 302 ASN C 50 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 299 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN I 166 HIS ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 HIS M 37 HIS M 149 GLN N 26 GLN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN Y 66 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS g 92 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 31 ASN t 8 GLN ** t 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 148782 Z= 0.208 Angle : 0.542 15.343 219691 Z= 0.275 Chirality : 0.033 0.255 27408 Planarity : 0.004 0.078 13321 Dihedral : 23.561 179.473 69312 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.95 % Rotamer: Outliers : 5.59 % Allowed : 23.35 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.10), residues: 6651 helix: 1.02 (0.11), residues: 2224 sheet: -0.91 (0.16), residues: 930 loop : -0.87 (0.11), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP t 170 HIS 0.007 0.001 HIS I 166 PHE 0.014 0.001 PHE B 102 TYR 0.037 0.002 TYR M 30 ARG 0.010 0.000 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1995 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1671 time to evaluate : 6.725 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: A 34 PHE cc_start: 0.8064 (t80) cc_final: 0.7760 (t80) REVERT: A 65 ASP cc_start: 0.8623 (t0) cc_final: 0.8281 (t0) REVERT: A 95 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: A 194 ASN cc_start: 0.8939 (t0) cc_final: 0.8560 (t0) REVERT: B 53 MET cc_start: 0.8390 (mtp) cc_final: 0.8126 (mtp) REVERT: B 97 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8203 (mtt180) REVERT: B 121 ASN cc_start: 0.8788 (t0) cc_final: 0.8285 (t0) REVERT: B 328 ASN cc_start: 0.7814 (m-40) cc_final: 0.7547 (m110) REVERT: B 332 MET cc_start: 0.7352 (ttt) cc_final: 0.6933 (ttt) REVERT: B 351 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 11 TYR cc_start: 0.8886 (m-80) cc_final: 0.8656 (m-80) REVERT: C 92 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8733 (p90) REVERT: C 94 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8129 (m110) REVERT: C 201 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8392 (mmm-85) REVERT: C 335 MET cc_start: 0.8451 (ttm) cc_final: 0.8065 (ttm) REVERT: D 34 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8420 (tttm) REVERT: D 152 ARG cc_start: 0.8703 (tpt170) cc_final: 0.8361 (tpt170) REVERT: D 212 MET cc_start: 0.8874 (mmm) cc_final: 0.8632 (mmm) REVERT: D 236 MET cc_start: 0.8080 (mtp) cc_final: 0.7826 (ptm) REVERT: E 115 TYR cc_start: 0.7951 (t80) cc_final: 0.7439 (t80) REVERT: E 205 ASP cc_start: 0.8223 (p0) cc_final: 0.7773 (p0) REVERT: E 207 LYS cc_start: 0.8879 (tptt) cc_final: 0.8541 (tppt) REVERT: E 245 GLN cc_start: 0.7888 (tp40) cc_final: 0.7653 (tp40) REVERT: E 274 GLN cc_start: 0.8659 (mt0) cc_final: 0.8385 (mt0) REVERT: E 282 TYR cc_start: 0.8930 (m-80) cc_final: 0.8618 (m-80) REVERT: F 193 GLU cc_start: 0.8272 (tp30) cc_final: 0.7952 (tp30) REVERT: F 247 MET cc_start: 0.8906 (mmm) cc_final: 0.8356 (ttm) REVERT: G 74 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (mm) REVERT: G 75 LYS cc_start: 0.8635 (mtmt) cc_final: 0.7829 (mtpp) REVERT: G 167 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9153 (t) REVERT: G 192 HIS cc_start: 0.5838 (t-90) cc_final: 0.5596 (t-170) REVERT: G 199 CYS cc_start: 0.8548 (t) cc_final: 0.8289 (t) REVERT: G 211 ASP cc_start: 0.8512 (m-30) cc_final: 0.8085 (m-30) REVERT: G 228 ASP cc_start: 0.8336 (t0) cc_final: 0.8096 (t0) REVERT: G 240 ASN cc_start: 0.9020 (t0) cc_final: 0.8468 (t0) REVERT: H 8 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7373 (tm-30) REVERT: H 92 MET cc_start: 0.8249 (mtp) cc_final: 0.7918 (mtm) REVERT: I 57 TYR cc_start: 0.8940 (t80) cc_final: 0.8606 (t80) REVERT: J 41 GLU cc_start: 0.8374 (tp30) cc_final: 0.7570 (tp30) REVERT: J 54 ARG cc_start: 0.7800 (tmt170) cc_final: 0.7545 (tmt170) REVERT: J 84 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8377 (tp30) REVERT: J 92 TYR cc_start: 0.8157 (m-10) cc_final: 0.7941 (m-10) REVERT: J 98 ASN cc_start: 0.8917 (m110) cc_final: 0.8470 (m110) REVERT: K 99 ASP cc_start: 0.9088 (t0) cc_final: 0.8729 (t0) REVERT: K 158 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7191 (ttm170) REVERT: L 6 TYR cc_start: 0.9025 (m-80) cc_final: 0.8645 (m-80) REVERT: L 99 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: L 104 MET cc_start: 0.8964 (ttm) cc_final: 0.8545 (ttp) REVERT: M 12 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8376 (mtt180) REVERT: M 68 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8532 (ttm170) REVERT: M 145 ASN cc_start: 0.8720 (t0) cc_final: 0.8128 (t0) REVERT: M 199 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8318 (mm-40) REVERT: N 71 TYR cc_start: 0.8794 (m-80) cc_final: 0.8575 (m-10) REVERT: N 96 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: N 100 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: N 169 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7839 (mtp180) REVERT: P 6 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7280 (ptm-80) REVERT: P 17 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: P 77 ASN cc_start: 0.8115 (t0) cc_final: 0.7808 (t0) REVERT: P 175 GLU cc_start: 0.8531 (mp0) cc_final: 0.8255 (mp0) REVERT: Q 147 ASP cc_start: 0.8961 (t0) cc_final: 0.8755 (t0) REVERT: Q 174 THR cc_start: 0.8176 (m) cc_final: 0.7913 (p) REVERT: R 8 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: R 111 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7530 (tm-30) REVERT: S 34 MET cc_start: 0.8174 (ppp) cc_final: 0.7569 (ppp) REVERT: S 64 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6878 (tm-30) REVERT: S 81 ARG cc_start: 0.8387 (mmt90) cc_final: 0.7930 (mmt90) REVERT: S 108 GLU cc_start: 0.8157 (tt0) cc_final: 0.7632 (tp30) REVERT: T 35 LYS cc_start: 0.8492 (mmpt) cc_final: 0.7968 (mttp) REVERT: V 69 ASN cc_start: 0.8853 (t0) cc_final: 0.8441 (t0) REVERT: W 42 TYR cc_start: 0.8988 (m-80) cc_final: 0.8748 (m-10) REVERT: W 120 GLU cc_start: 0.7897 (pp20) cc_final: 0.7597 (pp20) REVERT: X 18 TYR cc_start: 0.8988 (m-80) cc_final: 0.8206 (m-80) REVERT: X 80 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8647 (pp) REVERT: X 113 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8681 (tp30) REVERT: Y 61 TYR cc_start: 0.9114 (m-80) cc_final: 0.8505 (m-80) REVERT: Y 108 TYR cc_start: 0.9087 (m-80) cc_final: 0.8715 (m-80) REVERT: Z 3 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: a 57 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8641 (ttmt) REVERT: b 40 LYS cc_start: 0.8003 (mttm) cc_final: 0.7549 (mtmm) REVERT: b 79 ASN cc_start: 0.8528 (m-40) cc_final: 0.8120 (m-40) REVERT: b 101 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7312 (mmtp) REVERT: b 103 TYR cc_start: 0.8671 (p90) cc_final: 0.8305 (p90) REVERT: b 109 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9260 (m) REVERT: c 52 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8773 (mm110) REVERT: c 70 LEU cc_start: 0.9046 (mp) cc_final: 0.8815 (mt) REVERT: d 31 GLU cc_start: 0.8293 (tt0) cc_final: 0.8005 (tm-30) REVERT: d 38 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8044 (mt-10) REVERT: d 50 VAL cc_start: 0.9295 (t) cc_final: 0.8959 (p) REVERT: e 28 ASN cc_start: 0.8753 (t0) cc_final: 0.8499 (t0) REVERT: e 100 GLN cc_start: 0.8725 (tp40) cc_final: 0.8424 (tp-100) REVERT: f 22 ASP cc_start: 0.8394 (t0) cc_final: 0.7819 (p0) REVERT: f 27 GLU cc_start: 0.8107 (tp30) cc_final: 0.7527 (tp30) REVERT: f 108 GLN cc_start: 0.8625 (mt0) cc_final: 0.8295 (mt0) REVERT: g 43 MET cc_start: 0.7897 (tmm) cc_final: 0.7389 (tmm) REVERT: g 84 LYS cc_start: 0.8980 (mttm) cc_final: 0.8770 (mttm) REVERT: g 88 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8164 (mm-30) REVERT: j 15 LYS cc_start: 0.8651 (tttm) cc_final: 0.8152 (tttp) REVERT: j 36 ARG cc_start: 0.7121 (mtt180) cc_final: 0.6842 (mtt180) REVERT: k 114 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7881 (ptpt) REVERT: l 2 ARG cc_start: 0.8614 (ttt180) cc_final: 0.7566 (ttm170) REVERT: l 4 LYS cc_start: 0.8596 (tttt) cc_final: 0.6882 (mmtt) REVERT: l 10 MET cc_start: 0.8559 (tpp) cc_final: 0.8286 (tpp) REVERT: l 15 ARG cc_start: 0.8348 (ptt180) cc_final: 0.7907 (mtt-85) REVERT: l 21 ARG cc_start: 0.8477 (tpt-90) cc_final: 0.6720 (tpt170) REVERT: n 6 LYS cc_start: 0.8642 (tptt) cc_final: 0.8109 (tptt) REVERT: n 83 ILE cc_start: 0.9190 (mt) cc_final: 0.8932 (mt) REVERT: o 7 GLN cc_start: 0.9011 (mp10) cc_final: 0.8710 (mp10) REVERT: o 86 ASN cc_start: 0.9148 (t0) cc_final: 0.8769 (t0) REVERT: o 104 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8058 (ptp90) REVERT: o 133 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8353 (tmtt) REVERT: o 162 ARG cc_start: 0.6515 (ttm170) cc_final: 0.6000 (tmt170) REVERT: p 48 THR cc_start: 0.9045 (m) cc_final: 0.8765 (p) REVERT: p 64 MET cc_start: 0.8451 (mtp) cc_final: 0.8078 (mtp) REVERT: p 71 ARG cc_start: 0.7583 (ptt90) cc_final: 0.7323 (ptt90) REVERT: p 72 LYS cc_start: 0.8836 (mttp) cc_final: 0.8467 (mttp) REVERT: t 23 MET cc_start: 0.7939 (ttt) cc_final: 0.7713 (ttt) REVERT: t 55 MET cc_start: 0.8369 (ttm) cc_final: 0.8141 (ttm) REVERT: t 219 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: t 259 MET cc_start: 0.7220 (mtp) cc_final: 0.7012 (ttm) REVERT: t 271 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8538 (ttp-110) outliers start: 324 outliers final: 266 residues processed: 1821 average time/residue: 1.2140 time to fit residues: 3837.9354 Evaluate side-chains 1914 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1628 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 68 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 100 GLU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 4 SER Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 82 VAL Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 73 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain p residue 100 ASN Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 124 THR Chi-restraints excluded: chain t residue 135 VAL Chi-restraints excluded: chain t residue 164 THR Chi-restraints excluded: chain t residue 219 GLU Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 911 optimal weight: 8.9990 chunk 960 optimal weight: 10.0000 chunk 876 optimal weight: 8.9990 chunk 934 optimal weight: 10.0000 chunk 562 optimal weight: 7.9990 chunk 406 optimal weight: 9.9990 chunk 733 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 844 optimal weight: 10.0000 chunk 883 optimal weight: 50.0000 chunk 930 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 158 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS G 66 GLN H 78 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS M 149 GLN N 26 GLN N 50 ASN Q 91 HIS R 98 HIS ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN ** t 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.154 148782 Z= 0.577 Angle : 0.782 15.329 219691 Z= 0.392 Chirality : 0.044 0.313 27408 Planarity : 0.006 0.093 13321 Dihedral : 23.711 179.696 69311 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.34 % Rotamer: Outliers : 6.16 % Allowed : 23.44 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 6651 helix: 0.60 (0.11), residues: 2229 sheet: -1.00 (0.16), residues: 932 loop : -1.10 (0.11), residues: 3490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP t 170 HIS 0.048 0.002 HIS C 282 PHE 0.023 0.003 PHE F 37 TYR 0.034 0.003 TYR M 30 ARG 0.012 0.001 ARG O 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1967 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1610 time to evaluate : 8.874 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: A 65 ASP cc_start: 0.8744 (t0) cc_final: 0.8451 (t0) REVERT: A 194 ASN cc_start: 0.9050 (t0) cc_final: 0.8643 (t0) REVERT: B 70 LYS cc_start: 0.8527 (mttt) cc_final: 0.8319 (mtmm) REVERT: B 74 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: B 97 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8245 (mtt180) REVERT: B 121 ASN cc_start: 0.8755 (t0) cc_final: 0.8292 (t0) REVERT: B 328 ASN cc_start: 0.7999 (m-40) cc_final: 0.7609 (m110) REVERT: B 332 MET cc_start: 0.7805 (ttt) cc_final: 0.7230 (ttt) REVERT: B 351 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (mt) REVERT: C 13 GLU cc_start: 0.8532 (pp20) cc_final: 0.8204 (pp20) REVERT: C 94 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (m110) REVERT: C 101 MET cc_start: 0.8617 (ptm) cc_final: 0.8369 (ptm) REVERT: C 201 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8375 (mmm-85) REVERT: D 34 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8545 (tttm) REVERT: D 152 ARG cc_start: 0.8737 (tpt170) cc_final: 0.8382 (tpt170) REVERT: D 236 MET cc_start: 0.8383 (mtp) cc_final: 0.7996 (ptm) REVERT: E 115 TYR cc_start: 0.8143 (t80) cc_final: 0.7703 (t80) REVERT: E 205 ASP cc_start: 0.8345 (p0) cc_final: 0.7918 (p0) REVERT: E 207 LYS cc_start: 0.8853 (tptt) cc_final: 0.8480 (tppt) REVERT: F 57 TYR cc_start: 0.9123 (m-80) cc_final: 0.8915 (m-80) REVERT: F 110 GLN cc_start: 0.8996 (mt0) cc_final: 0.8770 (mt0) REVERT: F 193 GLU cc_start: 0.8414 (tp30) cc_final: 0.8047 (tp30) REVERT: F 247 MET cc_start: 0.8920 (mmm) cc_final: 0.8281 (ttm) REVERT: G 74 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8649 (mm) REVERT: G 75 LYS cc_start: 0.8670 (mtmt) cc_final: 0.7948 (mtpp) REVERT: G 117 ARG cc_start: 0.7616 (tpt170) cc_final: 0.7203 (tpt170) REVERT: G 167 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9364 (t) REVERT: G 192 HIS cc_start: 0.5996 (t-90) cc_final: 0.5715 (t-170) REVERT: G 199 CYS cc_start: 0.8698 (t) cc_final: 0.8356 (t) REVERT: G 211 ASP cc_start: 0.8525 (m-30) cc_final: 0.8109 (m-30) REVERT: G 228 ASP cc_start: 0.8392 (t0) cc_final: 0.8175 (t0) REVERT: G 240 ASN cc_start: 0.9034 (t0) cc_final: 0.8586 (t0) REVERT: H 92 MET cc_start: 0.8406 (mtp) cc_final: 0.8144 (mtm) REVERT: H 188 GLN cc_start: 0.8086 (mm110) cc_final: 0.7630 (mm-40) REVERT: J 41 GLU cc_start: 0.8367 (tp30) cc_final: 0.7581 (tp30) REVERT: J 140 SER cc_start: 0.9511 (m) cc_final: 0.9223 (t) REVERT: K 99 ASP cc_start: 0.9160 (t0) cc_final: 0.8923 (t0) REVERT: K 135 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7713 (mmtt) REVERT: K 158 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7205 (ttm170) REVERT: L 104 MET cc_start: 0.9042 (ttm) cc_final: 0.8669 (ttp) REVERT: M 68 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7356 (ttm170) REVERT: N 96 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: N 100 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: O 34 GLN cc_start: 0.8886 (tp40) cc_final: 0.8554 (tp40) REVERT: O 49 LYS cc_start: 0.8868 (mttm) cc_final: 0.8558 (mmmt) REVERT: P 17 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: P 96 PRO cc_start: 0.8879 (Cg_exo) cc_final: 0.8676 (Cg_endo) REVERT: P 150 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8206 (mtt-85) REVERT: P 175 GLU cc_start: 0.8463 (mp0) cc_final: 0.8175 (mp0) REVERT: Q 47 PHE cc_start: 0.9034 (m-80) cc_final: 0.8683 (m-80) REVERT: Q 66 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: R 8 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8030 (ttm170) REVERT: R 52 MET cc_start: 0.8865 (ptm) cc_final: 0.8243 (ttp) REVERT: R 111 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7625 (tm-30) REVERT: S 34 MET cc_start: 0.8113 (ppp) cc_final: 0.7763 (ppp) REVERT: S 64 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6911 (tm-30) REVERT: T 35 LYS cc_start: 0.8495 (mmpt) cc_final: 0.7955 (mmtp) REVERT: V 69 ASN cc_start: 0.9029 (t0) cc_final: 0.8806 (t0) REVERT: W 10 ASP cc_start: 0.8938 (t0) cc_final: 0.8317 (t70) REVERT: W 69 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7764 (tptt) REVERT: X 113 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8765 (tp30) REVERT: Y 61 TYR cc_start: 0.9198 (m-80) cc_final: 0.8652 (m-80) REVERT: Y 108 TYR cc_start: 0.9152 (m-80) cc_final: 0.8697 (m-80) REVERT: Z 3 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8573 (ttmm) REVERT: Z 11 ASN cc_start: 0.8449 (t0) cc_final: 0.8073 (t0) REVERT: a 57 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8746 (ttmt) REVERT: b 40 LYS cc_start: 0.8162 (mttm) cc_final: 0.7744 (mtmm) REVERT: b 57 MET cc_start: 0.8283 (mmp) cc_final: 0.8047 (mmm) REVERT: b 79 ASN cc_start: 0.8839 (m-40) cc_final: 0.8468 (m-40) REVERT: b 101 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7292 (mmtp) REVERT: b 103 TYR cc_start: 0.8714 (p90) cc_final: 0.8508 (p90) REVERT: c 52 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8951 (mm-40) REVERT: c 70 LEU cc_start: 0.9097 (mp) cc_final: 0.8872 (mt) REVERT: c 86 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: d 38 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8000 (mt-10) REVERT: d 104 MET cc_start: 0.8399 (mmt) cc_final: 0.7945 (mmt) REVERT: e 28 ASN cc_start: 0.8860 (t0) cc_final: 0.8657 (t0) REVERT: e 100 GLN cc_start: 0.8700 (tp40) cc_final: 0.8190 (tp-100) REVERT: f 27 GLU cc_start: 0.8111 (tp30) cc_final: 0.7340 (tp30) REVERT: f 87 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8198 (ptpp) REVERT: f 108 GLN cc_start: 0.8669 (mt0) cc_final: 0.8340 (mt0) REVERT: g 43 MET cc_start: 0.8265 (tmm) cc_final: 0.7706 (tmm) REVERT: j 17 GLN cc_start: 0.8597 (tt0) cc_final: 0.8129 (tt0) REVERT: j 36 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6926 (mtt180) REVERT: k 114 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7947 (ptpt) REVERT: l 2 ARG cc_start: 0.8591 (ttt180) cc_final: 0.7543 (ttm170) REVERT: l 4 LYS cc_start: 0.8582 (tttt) cc_final: 0.6593 (mmtt) REVERT: l 15 ARG cc_start: 0.8357 (ptt180) cc_final: 0.7835 (mtt-85) REVERT: l 21 ARG cc_start: 0.8314 (tpt-90) cc_final: 0.6696 (tpt170) REVERT: n 6 LYS cc_start: 0.8664 (tptt) cc_final: 0.8065 (tptt) REVERT: n 83 ILE cc_start: 0.9236 (mt) cc_final: 0.9007 (mt) REVERT: o 25 ASP cc_start: 0.8360 (t70) cc_final: 0.8043 (t70) REVERT: o 86 ASN cc_start: 0.9177 (t0) cc_final: 0.8864 (t0) REVERT: o 104 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7834 (ptp90) REVERT: o 162 ARG cc_start: 0.6515 (ttm170) cc_final: 0.5988 (tmt170) REVERT: p 28 GLU cc_start: 0.7916 (mp0) cc_final: 0.7283 (mp0) REVERT: p 64 MET cc_start: 0.8624 (mtp) cc_final: 0.8357 (mtp) REVERT: p 71 ARG cc_start: 0.7897 (ptt90) cc_final: 0.7345 (ptt90) REVERT: p 72 LYS cc_start: 0.9016 (mttp) cc_final: 0.8753 (mttp) REVERT: t 88 HIS cc_start: 0.8610 (m-70) cc_final: 0.8232 (m-70) REVERT: t 259 MET cc_start: 0.7174 (mtp) cc_final: 0.6786 (ttm) REVERT: t 271 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8714 (ttp-110) outliers start: 357 outliers final: 303 residues processed: 1792 average time/residue: 1.2281 time to fit residues: 3820.9353 Evaluate side-chains 1907 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1586 time to evaluate : 6.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 66 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 68 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 100 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 66 GLN Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 132 ILE Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 69 LYS Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 65 ARG Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 82 VAL Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 91 CYS Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 91 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain j residue 34 LYS Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 16 THR Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 33 GLN Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 124 THR Chi-restraints excluded: chain t residue 164 THR Chi-restraints excluded: chain t residue 189 GLN Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 613 optimal weight: 1.9990 chunk 987 optimal weight: 10.0000 chunk 602 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 chunk 686 optimal weight: 6.9990 chunk 1036 optimal weight: 7.9990 chunk 953 optimal weight: 8.9990 chunk 825 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 637 optimal weight: 8.9990 chunk 505 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 213 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN ** Y 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN t 8 GLN t 123 HIS ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 148782 Z= 0.244 Angle : 0.587 14.418 219691 Z= 0.298 Chirality : 0.035 0.310 27408 Planarity : 0.005 0.085 13321 Dihedral : 23.672 179.679 69311 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 5.04 % Allowed : 24.62 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 6651 helix: 0.90 (0.11), residues: 2218 sheet: -0.96 (0.16), residues: 926 loop : -0.95 (0.11), residues: 3507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP t 170 HIS 0.033 0.001 HIS C 282 PHE 0.016 0.001 PHE j 12 TYR 0.048 0.002 TYR M 30 ARG 0.015 0.001 ARG G 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13302 Ramachandran restraints generated. 6651 Oldfield, 0 Emsley, 6651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1947 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1655 time to evaluate : 6.606 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: A 65 ASP cc_start: 0.8664 (t0) cc_final: 0.8365 (t70) REVERT: A 194 ASN cc_start: 0.8903 (t0) cc_final: 0.8563 (t0) REVERT: B 97 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8236 (mtt180) REVERT: B 121 ASN cc_start: 0.8771 (t0) cc_final: 0.8289 (t0) REVERT: B 328 ASN cc_start: 0.7817 (m-40) cc_final: 0.7536 (m110) REVERT: B 332 MET cc_start: 0.7489 (ttt) cc_final: 0.7034 (ttt) REVERT: B 351 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 13 GLU cc_start: 0.8490 (pp20) cc_final: 0.8135 (pp20) REVERT: C 94 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8235 (m110) REVERT: C 101 MET cc_start: 0.8619 (ptm) cc_final: 0.8313 (ptm) REVERT: C 201 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: D 34 LYS cc_start: 0.8753 (tmtt) cc_final: 0.8330 (tttm) REVERT: D 152 ARG cc_start: 0.8777 (tpt170) cc_final: 0.8457 (tpt170) REVERT: D 236 MET cc_start: 0.8156 (mtp) cc_final: 0.7832 (ptm) REVERT: E 115 TYR cc_start: 0.8085 (t80) cc_final: 0.7576 (t80) REVERT: E 205 ASP cc_start: 0.8243 (p0) cc_final: 0.7657 (p0) REVERT: E 207 LYS cc_start: 0.8791 (tptt) cc_final: 0.8439 (tppt) REVERT: E 274 GLN cc_start: 0.8672 (mt0) cc_final: 0.8391 (mt0) REVERT: E 282 TYR cc_start: 0.8974 (m-80) cc_final: 0.8624 (m-80) REVERT: F 193 GLU cc_start: 0.8295 (tp30) cc_final: 0.7972 (tp30) REVERT: F 247 MET cc_start: 0.8914 (mmm) cc_final: 0.8390 (ttm) REVERT: G 74 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8512 (mm) REVERT: G 75 LYS cc_start: 0.8594 (mtmt) cc_final: 0.7778 (mtpp) REVERT: G 117 ARG cc_start: 0.7605 (tpt170) cc_final: 0.7218 (tpt170) REVERT: G 167 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9086 (t) REVERT: G 192 HIS cc_start: 0.5883 (t-90) cc_final: 0.5632 (t-170) REVERT: G 199 CYS cc_start: 0.8581 (t) cc_final: 0.8307 (t) REVERT: G 211 ASP cc_start: 0.8455 (m-30) cc_final: 0.8071 (m-30) REVERT: G 228 ASP cc_start: 0.8336 (t0) cc_final: 0.8106 (t0) REVERT: G 240 ASN cc_start: 0.9028 (t0) cc_final: 0.8513 (t0) REVERT: H 8 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 92 MET cc_start: 0.8222 (mtp) cc_final: 0.7946 (mtm) REVERT: I 57 TYR cc_start: 0.8924 (t80) cc_final: 0.8577 (t80) REVERT: J 84 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8363 (tp30) REVERT: J 92 TYR cc_start: 0.8314 (m-10) cc_final: 0.8023 (m-10) REVERT: J 98 ASN cc_start: 0.8957 (m110) cc_final: 0.8507 (m110) REVERT: K 5 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7494 (mtt90) REVERT: K 99 ASP cc_start: 0.9101 (t0) cc_final: 0.8752 (t0) REVERT: K 158 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7165 (ttm170) REVERT: L 6 TYR cc_start: 0.9037 (m-80) cc_final: 0.8657 (m-80) REVERT: L 99 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: L 104 MET cc_start: 0.8994 (ttm) cc_final: 0.8578 (ttp) REVERT: M 12 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8374 (mtt180) REVERT: M 68 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8648 (ttm170) REVERT: M 145 ASN cc_start: 0.8781 (t0) cc_final: 0.8213 (t0) REVERT: M 199 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8273 (mm-40) REVERT: N 71 TYR cc_start: 0.8858 (m-80) cc_final: 0.8643 (m-10) REVERT: N 81 TRP cc_start: 0.9224 (t60) cc_final: 0.9003 (t60) REVERT: N 96 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7668 (mm110) REVERT: N 100 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: N 169 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7900 (mtm180) REVERT: O 34 GLN cc_start: 0.8819 (tp40) cc_final: 0.8518 (tp40) REVERT: P 6 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7239 (ptm-80) REVERT: P 17 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: P 150 ARG cc_start: 0.8549 (mmt90) cc_final: 0.8343 (mtt-85) REVERT: P 175 GLU cc_start: 0.8542 (mp0) cc_final: 0.8261 (mp0) REVERT: Q 66 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: R 8 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7701 (ttm170) REVERT: R 111 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7422 (tm-30) REVERT: S 34 MET cc_start: 0.8159 (ppp) cc_final: 0.7822 (ppp) REVERT: S 64 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6699 (tm-30) REVERT: S 70 ILE cc_start: 0.9273 (mm) cc_final: 0.9063 (mm) REVERT: T 35 LYS cc_start: 0.8488 (mmpt) cc_final: 0.7965 (mmtp) REVERT: V 69 ASN cc_start: 0.8875 (t0) cc_final: 0.8577 (t0) REVERT: W 1 MET cc_start: 0.7931 (tpp) cc_final: 0.7671 (tpt) REVERT: W 42 TYR cc_start: 0.8967 (m-80) cc_final: 0.8740 (m-10) REVERT: X 18 TYR cc_start: 0.8964 (m-80) cc_final: 0.8125 (m-80) REVERT: X 113 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8710 (tp30) REVERT: Y 61 TYR cc_start: 0.9130 (m-80) cc_final: 0.8523 (m-80) REVERT: Y 89 ASN cc_start: 0.8872 (m-40) cc_final: 0.8589 (m110) REVERT: Y 108 TYR cc_start: 0.9084 (m-80) cc_final: 0.8789 (m-80) REVERT: Y 120 GLN cc_start: 0.8594 (mt0) cc_final: 0.8343 (mt0) REVERT: Z 3 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: Z 68 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7537 (mtt180) REVERT: a 57 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8662 (ttmt) REVERT: b 40 LYS cc_start: 0.8072 (mttm) cc_final: 0.7638 (mtmm) REVERT: b 54 MET cc_start: 0.8102 (mmm) cc_final: 0.7900 (mmm) REVERT: b 79 ASN cc_start: 0.8604 (m-40) cc_final: 0.8168 (m-40) REVERT: b 103 TYR cc_start: 0.8667 (p90) cc_final: 0.8306 (p90) REVERT: c 52 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8806 (mm110) REVERT: c 70 LEU cc_start: 0.9087 (mp) cc_final: 0.8852 (mt) REVERT: c 86 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: d 31 GLU cc_start: 0.8261 (tt0) cc_final: 0.7976 (tm-30) REVERT: d 38 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8069 (mt-10) REVERT: e 28 ASN cc_start: 0.8779 (t0) cc_final: 0.8553 (t0) REVERT: e 100 GLN cc_start: 0.8718 (tp40) cc_final: 0.8421 (tp-100) REVERT: f 27 GLU cc_start: 0.8059 (tp30) cc_final: 0.7300 (tp30) REVERT: f 87 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7999 (ptpp) REVERT: f 108 GLN cc_start: 0.8630 (mt0) cc_final: 0.8307 (mt0) REVERT: g 43 MET cc_start: 0.7971 (tmm) cc_final: 0.7452 (tmm) REVERT: g 68 ARG cc_start: 0.7450 (tpt90) cc_final: 0.7163 (ttt90) REVERT: j 36 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6267 (mtm180) REVERT: k 114 LYS cc_start: 0.8138 (ptmt) cc_final: 0.7867 (ptpt) REVERT: l 2 ARG cc_start: 0.8628 (ttt180) cc_final: 0.7614 (ttm170) REVERT: l 4 LYS cc_start: 0.8617 (tttt) cc_final: 0.6710 (mmtt) REVERT: l 10 MET cc_start: 0.8528 (tpp) cc_final: 0.8318 (tpp) REVERT: l 15 ARG cc_start: 0.8316 (ptt180) cc_final: 0.7888 (mtt-85) REVERT: l 21 ARG cc_start: 0.8315 (tpt-90) cc_final: 0.6731 (tpt170) REVERT: m 6 LYS cc_start: 0.8809 (tppp) cc_final: 0.8556 (tppp) REVERT: n 6 LYS cc_start: 0.8718 (tptt) cc_final: 0.8173 (tptt) REVERT: n 83 ILE cc_start: 0.9198 (mt) cc_final: 0.8942 (mt) REVERT: o 7 GLN cc_start: 0.9022 (mp10) cc_final: 0.8741 (mp10) REVERT: o 86 ASN cc_start: 0.9144 (t0) cc_final: 0.8777 (t0) REVERT: o 104 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8056 (ptp90) REVERT: o 133 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8399 (tmtt) REVERT: o 162 ARG cc_start: 0.6636 (ttm170) cc_final: 0.6108 (tmt170) REVERT: p 28 GLU cc_start: 0.7748 (mp0) cc_final: 0.7457 (mp0) REVERT: p 48 THR cc_start: 0.9061 (m) cc_final: 0.8842 (p) REVERT: p 64 MET cc_start: 0.8545 (mtp) cc_final: 0.8218 (mtp) REVERT: p 71 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7453 (ppt90) REVERT: p 72 LYS cc_start: 0.8892 (mttp) cc_final: 0.8556 (mttp) REVERT: t 55 MET cc_start: 0.8330 (ttm) cc_final: 0.8035 (ttp) REVERT: t 88 HIS cc_start: 0.8565 (m-70) cc_final: 0.8222 (m-70) REVERT: t 259 MET cc_start: 0.7336 (mtp) cc_final: 0.7053 (ttm) REVERT: t 271 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8587 (ttp-110) REVERT: t 315 PHE cc_start: 0.6953 (m-10) cc_final: 0.6640 (m-10) outliers start: 292 outliers final: 258 residues processed: 1796 average time/residue: 1.2837 time to fit residues: 3993.0638 Evaluate side-chains 1898 residues out of total 5804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1622 time to evaluate : 6.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 66 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 68 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain N residue 100 GLU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 70 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 188 ASN Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 66 GLN Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 110 TYR Chi-restraints excluded: chain S residue 114 TYR Chi-restraints excluded: chain S residue 115 PHE Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 28 ASN Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 94 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 78 ASN Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 105 ILE Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 100 ASN Chi-restraints excluded: chain b residue 109 VAL Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 11 LYS Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 25 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 64 LYS Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 91 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 71 GLN Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 53 SER Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 12 ASN Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain h residue 6 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 28 ASN Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain j residue 49 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 56 HIS Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 14 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 78 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 104 ARG Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain p residue 14 SER Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain t residue 39 SER Chi-restraints excluded: chain t residue 81 SER Chi-restraints excluded: chain t residue 112 VAL Chi-restraints excluded: chain t residue 124 THR Chi-restraints excluded: chain t residue 164 THR Chi-restraints excluded: chain t residue 189 GLN Chi-restraints excluded: chain t residue 220 VAL Chi-restraints excluded: chain t residue 271 ARG Chi-restraints excluded: chain t residue 274 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 306 ASN Chi-restraints excluded: chain t residue 308 LEU Chi-restraints excluded: chain t residue 322 THR Chi-restraints excluded: chain t residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 655 optimal weight: 10.0000 chunk 878 optimal weight: 8.9990 chunk 252 optimal weight: 3.9990 chunk 760 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 826 optimal weight: 10.0000 chunk 345 optimal weight: 0.7980 chunk 848 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN H 78 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS N 26 GLN O 97 ASN P 77 ASN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN Y 66 ASN Y 120 GLN ** c 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN g 92 ASN h 13 ASN m 45 GLN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 83 ASN t 8 GLN ** t 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087242 restraints weight = 284774.225| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.39 r_work: 0.3142 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 148782 Z= 0.311 Angle : 0.610 14.281 219691 Z= 0.310 Chirality : 0.036 0.310 27408 Planarity : 0.005 0.092 13321 Dihedral : 23.649 179.459 69311 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 5.47 % Allowed : 24.56 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 6651 helix: 0.90 (0.11), residues: 2222 sheet: -0.93 (0.16), residues: 925 loop : -0.95 (0.11), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP t 170 HIS 0.021 0.001 HIS g 80 PHE 0.018 0.002 PHE F 81 TYR 0.047 0.002 TYR M 30 ARG 0.009 0.001 ARG Q 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53843.33 seconds wall clock time: 929 minutes 38.02 seconds (55778.02 seconds total)