Starting phenix.real_space_refine on Sun Apr 14 21:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsp_35001/04_2024/8hsp_35001_updated.pdb" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 K 1 8.98 5 P 4554 5.49 5 Mg 315 5.21 5 S 151 5.16 5 C 71052 2.51 5 N 26410 2.21 5 O 39394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "N ASP 54": "OD1" <-> "OD2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O ASP 74": "OD1" <-> "OD2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "e ASP 154": "OD1" <-> "OD2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "j GLU 121": "OE1" <-> "OE2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 81": "OD1" <-> "OD2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m ASP 72": "OD1" <-> "OD2" Residue "n TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n ASP 93": "OD1" <-> "OD2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "p GLU 89": "OE1" <-> "OE2" Residue "p ASP 91": "OD1" <-> "OD2" Residue "q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t ASP 81": "OD1" <-> "OD2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "v GLU 17": "OE1" <-> "OE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "w PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "x GLU 59": "OE1" <-> "OE2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "z ASP 31": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141877 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 139, 'rna3p': 16, 'rna3p_pur': 1318, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "V" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 8, 'rna3p': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "W" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "X" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1647 Classifications: {'RNA': 76} Modifications used: {'rna2p': 4, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 12, 'rna3p': 63} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Unusual residues: {' K': 1, ' MG': 93} Classifications: {'undetermined': 94} Link IDs: {None: 93} Chain: "a" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Unusual residues: {' MG': 208} Classifications: {'undetermined': 208} Link IDs: {None: 207} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 55.07, per 1000 atoms: 0.39 Number of scatterers: 141877 At special positions: 0 Unit cell: (251.864, 235.294, 252.692, 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) K 1 19.00 S 151 16.00 P 4554 15.00 Mg 315 11.99 O 39394 8.00 N 26410 7.00 C 71052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.82 Conformation dependent library (CDL) restraints added in 6.8 seconds 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10260 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 170 helices and 73 sheets defined 38.9% alpha, 19.4% beta 1598 base pairs and 2396 stacking pairs defined. Time for finding SS restraints: 75.55 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.310A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.922A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.160A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 5.887A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.831A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 4.180A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 removed outlier: 3.683A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.884A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.647A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.526A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.279A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 4.006A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.709A pdb=" N GLY D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.920A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.598A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.707A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.576A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.217A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.335A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.565A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 Proline residue: F 19 - end of helix removed outlier: 3.752A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.615A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.566A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.057A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.657A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 153 removed outlier: 3.783A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N HIS G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 removed outlier: 3.569A pdb=" N GLY H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.627A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.717A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.144A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.914A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.561A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.865A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 93 through 104 removed outlier: 4.185A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.525A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.792A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 4.362A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 64 removed outlier: 4.441A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.726A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.508A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 removed outlier: 4.073A pdb=" N ASP N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.192A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.739A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 4.095A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 4.143A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY R 17 " --> pdb=" O PHE R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 17' Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.438A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.569A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 43 through 63 removed outlier: 3.559A pdb=" N ALA T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.899A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.650A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.976A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.019A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.703A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.861A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.984A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.853A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.045A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 Processing helix chain 'd' and resid 97 through 103 removed outlier: 4.837A pdb=" N PHE d 101 " --> pdb=" O SER d 97 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 97 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 removed outlier: 3.520A pdb=" N PHE e 19 " --> pdb=" O SER e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.557A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.357A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.587A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.728A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.358A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.719A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 5.566A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.635A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.729A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE f 138 " --> pdb=" O GLN f 135 " (cutoff:3.500A) Proline residue: f 139 - end of helix No H-bonds generated for 'chain 'f' and resid 134 through 139' Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.459A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.343A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.335A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 123 removed outlier: 3.894A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.743A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.726A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.586A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.664A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 83 removed outlier: 4.020A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 83' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.961A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 removed outlier: 4.321A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.517A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.459A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.085A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.509A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 60 Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 removed outlier: 3.529A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.590A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.622A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.700A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.689A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.720A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.754A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 4.284A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.604A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 3.600A pdb=" N LEU s 7 " --> pdb=" O ARG s 3 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.906A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.685A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.651A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.196A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU u 59 " --> pdb=" O GLU u 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 54 through 59' Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 4.848A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.634A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.379A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.858A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.267A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.767A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.492A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 3.904A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.854A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.522A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.912A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 181 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 172 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.709A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.665A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.512A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.766A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.390A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 91 " --> pdb=" O THR G 72 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.336A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU H 58 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 4.194A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.748A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.644A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG J 72 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER J 101 " --> pdb=" O ARG J 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG J 9 " --> pdb=" O GLN J 99 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP J 97 " --> pdb=" O LYS J 11 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 53 removed outlier: 8.514A pdb=" N ALA J 61 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 30 through 36 Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.232A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY L 85 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG L 94 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 35 through 41 removed outlier: 5.208A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.527A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'Q' and resid 56 through 59 removed outlier: 7.332A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'S' and resid 48 through 52 Processing sheet with id= 24, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.592A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.539A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.336A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.414A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 11 through 17 removed outlier: 4.011A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 32 through 35 removed outlier: 6.573A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 31, first strand: chain 'd' and resid 24 through 28 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.997A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.607A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.489A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 44 through 47 removed outlier: 6.960A pdb=" N ARG e 44 " --> pdb=" O PRO e 89 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA e 87 " --> pdb=" O GLN e 46 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 117 through 120 removed outlier: 3.865A pdb=" N LYS e 185 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.531A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS f 87 " --> pdb=" O MET f 38 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.839A pdb=" N LYS f 72 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN f 81 " --> pdb=" O LYS f 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 15 through 19 removed outlier: 3.527A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 82 through 89 removed outlier: 5.958A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 94 through 98 Processing sheet with id= 42, first strand: chain 'h' and resid 1 through 4 Processing sheet with id= 43, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 44, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.424A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.055A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 68 through 71 removed outlier: 3.964A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.844A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.867A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'l' and resid 30 through 36 removed outlier: 8.023A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.046A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'n' and resid 49 through 53 removed outlier: 3.533A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.496A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.688A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.573A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.076A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 58, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 59, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.181A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 2 through 8 removed outlier: 6.896A pdb=" N VAL r 106 " --> pdb=" O THR r 72 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 81 through 88 removed outlier: 3.879A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 28 through 33 removed outlier: 5.493A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 83 through 86 Processing sheet with id= 64, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.710A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.058A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'v' and resid 66 through 72 removed outlier: 3.512A pdb=" N ARG v 77 " --> pdb=" O LYS v 72 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.442A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.239A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.198A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '0' and resid 19 through 25 removed outlier: 6.365A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '2' and resid 22 through 25 removed outlier: 5.730A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 73, first strand: chain '4' and resid 12 through 15 No H-bonds generated for sheet with id= 73 1864 hydrogen bonds defined for protein. 5523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4019 hydrogen bonds 6294 hydrogen bond angles 0 basepair planarities 1598 basepair parallelities 2396 stacking parallelities Total time for adding SS restraints: 267.18 Time building geometry restraints manager: 62.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11452 1.29 - 1.43: 70191 1.43 - 1.57: 62859 1.57 - 1.71: 9110 1.71 - 1.85: 264 Bond restraints: 153876 Sorted by residual: bond pdb=" C5 5MU V 54 " pdb=" C6 5MU V 54 " ideal model delta sigma weight residual 1.155 1.452 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C5 5MU X 54 " pdb=" C6 5MU X 54 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.448 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.447 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.580 0.249 2.00e-02 2.50e+03 1.54e+02 ... (remaining 153871 not shown) Histogram of bond angle deviations from ideal: 97.23 - 106.54: 27827 106.54 - 115.85: 104750 115.85 - 125.15: 80145 125.15 - 134.46: 17547 134.46 - 143.77: 4 Bond angle restraints: 230273 Sorted by residual: angle pdb=" C1' 2MA V 38 " pdb=" N9 2MA V 38 " pdb=" C8 2MA V 38 " ideal model delta sigma weight residual 106.32 143.77 -37.45 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.25 -34.93 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C1' 2MA V 38 " pdb=" N9 2MA V 38 " pdb=" C4 2MA V 38 " ideal model delta sigma weight residual 138.88 108.79 30.09 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 111.55 27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 131.67 -21.60 3.00e+00 1.11e-01 5.18e+01 ... (remaining 230268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 87222 35.70 - 71.40: 9906 71.40 - 107.10: 1282 107.10 - 142.80: 14 142.80 - 178.51: 10 Dihedral angle restraints: 98434 sinusoidal: 82529 harmonic: 15905 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual 180.00 -133.59 -46.41 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 51.49 148.51 1 1.50e+01 4.44e-03 7.90e+01 ... (remaining 98431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 27108 0.070 - 0.141: 2019 0.141 - 0.211: 151 0.211 - 0.282: 22 0.282 - 0.352: 6 Chirality restraints: 29306 Sorted by residual: chirality pdb=" CA MEQ d 150 " pdb=" N MEQ d 150 " pdb=" C MEQ d 150 " pdb=" CB MEQ d 150 " both_signs ideal model delta sigma weight residual False 2.38 2.73 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C3' G W 30 " pdb=" C4' G W 30 " pdb=" O3' G W 30 " pdb=" C2' G W 30 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C2' 3TD a1915 " pdb=" C3' 3TD a1915 " pdb=" O2' 3TD a1915 " pdb=" C1' 3TD a1915 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 29303 not shown) Planarity restraints: 12254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.054 2.00e-02 2.50e+03 6.07e-01 8.28e+03 pdb=" C4' 2MG A1207 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.695 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.624 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.195 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.952 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.208 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.945 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.075 2.00e-02 2.50e+03 6.06e-01 8.28e+03 pdb=" C4' 2MG A1516 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.609 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.662 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.156 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.005 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.225 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.932 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.071 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 5MC A1407 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.600 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.165 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.995 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.228 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.910 2.00e-02 2.50e+03 ... (remaining 12251 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 787 2.50 - 3.16: 106401 3.16 - 3.82: 340340 3.82 - 4.48: 478746 4.48 - 5.14: 626219 Nonbonded interactions: 1552493 Sorted by model distance: nonbonded pdb=" OP2 A a 621 " pdb="MG MG a6016 " model vdw 1.843 2.170 nonbonded pdb=" OP1 A a 761 " pdb="MG MG a6085 " model vdw 1.851 2.170 nonbonded pdb=" OP1 U a 120 " pdb="MG MG a6003 " model vdw 1.856 2.170 nonbonded pdb=" OP2 U a 963 " pdb="MG MG a6030 " model vdw 1.861 2.170 nonbonded pdb=" OP1 U a 419 " pdb="MG MG a6005 " model vdw 1.891 2.170 ... (remaining 1552488 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: 7.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 34.800 Check model and map are aligned: 1.490 Set scattering table: 0.930 Process input model: 553.360 Find NCS groups from input model: 2.710 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: 0.020 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 613.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 153876 Z= 0.333 Angle : 0.697 37.448 230273 Z= 0.349 Chirality : 0.039 0.352 29306 Planarity : 0.022 0.607 12254 Dihedral : 22.605 178.505 88174 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 0.02 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5474 helix: 0.99 (0.12), residues: 1849 sheet: -0.25 (0.15), residues: 1088 loop : -0.62 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 23 HIS 0.010 0.001 HIS 2 31 PHE 0.018 0.002 PHE d 118 TYR 0.021 0.002 TYR r 38 ARG 0.014 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1085 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 8 ILE cc_start: 0.6651 (mm) cc_final: 0.6354 (mm) REVERT: J 88 MET cc_start: 0.4622 (mmp) cc_final: 0.4154 (tpp) REVERT: Q 41 THR cc_start: 0.7670 (m) cc_final: 0.7375 (m) REVERT: f 17 MET cc_start: 0.6238 (mmm) cc_final: 0.5972 (mtp) REVERT: r 55 ILE cc_start: 0.8266 (mt) cc_final: 0.8014 (mp) REVERT: w 54 LYS cc_start: 0.7945 (tttm) cc_final: 0.7744 (tmtp) outliers start: 1 outliers final: 1 residues processed: 1086 average time/residue: 2.3462 time to fit residues: 3533.7877 Evaluate side-chains 908 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 907 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 6.9990 chunk 748 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 505 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 774 optimal weight: 8.9990 chunk 299 optimal weight: 0.6980 chunk 470 optimal weight: 30.0000 chunk 576 optimal weight: 10.0000 chunk 897 optimal weight: 7.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN C 139 GLN D 40 GLN D 71 GLN D 89 ASN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN L 5 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN P 26 ASN P 29 ASN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 78 ASN c 115 GLN e 163 ASN g 104 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN q 6 GLN s 70 HIS ** u 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 153876 Z= 0.314 Angle : 0.787 17.085 230273 Z= 0.414 Chirality : 0.042 0.365 29306 Planarity : 0.008 0.147 12254 Dihedral : 23.056 179.850 77148 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 3.17 % Allowed : 10.91 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5474 helix: 0.98 (0.12), residues: 1857 sheet: -0.17 (0.16), residues: 1059 loop : -0.70 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.014 0.002 HIS 2 31 PHE 0.027 0.002 PHE F 8 TYR 0.018 0.002 TYR p 32 ARG 0.009 0.001 ARG c 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 932 time to evaluate : 6.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6509 (mmt) REVERT: D 89 ASN cc_start: 0.6992 (m-40) cc_final: 0.6658 (m-40) REVERT: E 26 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7046 (ptpp) REVERT: Q 30 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7321 (ttpm) REVERT: Q 38 ILE cc_start: 0.7793 (pt) cc_final: 0.7540 (pt) REVERT: d 202 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8348 (mp) REVERT: f 17 MET cc_start: 0.6303 (mmm) cc_final: 0.6023 (mtp) REVERT: f 20 PHE cc_start: 0.7204 (m-80) cc_final: 0.6972 (m-80) REVERT: i 95 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6460 (mtm180) REVERT: l 111 GLU cc_start: 0.6365 (mp0) cc_final: 0.6163 (mp0) REVERT: m 74 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: o 27 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: t 10 GLU cc_start: 0.6437 (tp30) cc_final: 0.6214 (tp30) REVERT: t 46 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: 3 18 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7785 (ttmt) outliers start: 145 outliers final: 69 residues processed: 991 average time/residue: 2.3058 time to fit residues: 3179.1119 Evaluate side-chains 969 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 891 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 161 MET Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain t residue 46 GLN Chi-restraints excluded: chain u residue 73 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 3 residue 18 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 746 optimal weight: 20.0000 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 898 optimal weight: 20.0000 chunk 970 optimal weight: 8.9990 chunk 800 optimal weight: 4.9990 chunk 891 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 721 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 116 GLN D 198 HIS E 70 ASN F 11 HIS F 37 HIS G 52 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 40 GLN O 62 GLN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 78 ASN c 251 GLN g 104 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN q 6 GLN s 70 HIS ** u 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 36 GLN ** 0 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 153876 Z= 0.185 Angle : 0.654 14.311 230273 Z= 0.359 Chirality : 0.036 0.382 29306 Planarity : 0.007 0.134 12254 Dihedral : 22.933 179.057 77148 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 3.52 % Allowed : 13.12 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.11), residues: 5474 helix: 1.32 (0.12), residues: 1867 sheet: -0.13 (0.16), residues: 1060 loop : -0.58 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 42 HIS 0.009 0.001 HIS P 59 PHE 0.019 0.002 PHE f 77 TYR 0.016 0.002 TYR G 44 ARG 0.008 0.000 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 938 time to evaluate : 5.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6773 (mmp) cc_final: 0.6503 (mmt) REVERT: D 89 ASN cc_start: 0.6952 (m-40) cc_final: 0.6677 (m-40) REVERT: E 26 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7079 (ptpp) REVERT: Q 30 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7268 (ttpm) REVERT: Q 38 ILE cc_start: 0.7764 (pt) cc_final: 0.7550 (pt) REVERT: T 40 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5759 (tm-30) REVERT: T 55 GLN cc_start: 0.5798 (OUTLIER) cc_final: 0.5584 (tt0) REVERT: U 3 VAL cc_start: 0.6870 (OUTLIER) cc_final: 0.6517 (t) REVERT: f 17 MET cc_start: 0.6399 (mmm) cc_final: 0.6089 (mtp) REVERT: f 20 PHE cc_start: 0.7126 (m-80) cc_final: 0.6891 (m-80) REVERT: h 1 MET cc_start: 0.5105 (OUTLIER) cc_final: 0.3822 (ppp) REVERT: i 95 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6501 (mtm180) REVERT: j 1 MET cc_start: 0.7970 (ttm) cc_final: 0.7514 (ttm) REVERT: m 30 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: o 13 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6616 (ptm) REVERT: o 27 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: r 73 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7232 (mttm) REVERT: t 10 GLU cc_start: 0.6422 (tp30) cc_final: 0.6193 (tp30) REVERT: v 72 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7091 (pttm) REVERT: 3 18 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7738 (ttmt) outliers start: 161 outliers final: 73 residues processed: 1009 average time/residue: 2.2277 time to fit residues: 3156.6465 Evaluate side-chains 972 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 887 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 48 ILE Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 0.9990 chunk 675 optimal weight: 0.1980 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 428 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 2.9990 chunk 955 optimal weight: 0.7980 chunk 471 optimal weight: 30.0000 chunk 854 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN O 62 GLN T 13 GLN T 78 ASN c 251 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS ** 0 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 153876 Z= 0.163 Angle : 0.636 14.008 230273 Z= 0.351 Chirality : 0.035 0.390 29306 Planarity : 0.006 0.133 12254 Dihedral : 22.911 178.973 77146 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.43 % Allowed : 14.74 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 5474 helix: 1.44 (0.12), residues: 1873 sheet: -0.09 (0.16), residues: 1074 loop : -0.55 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 42 HIS 0.008 0.001 HIS F 11 PHE 0.019 0.001 PHE w 46 TYR 0.015 0.001 TYR r 38 ARG 0.007 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 902 time to evaluate : 6.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6797 (mmp) cc_final: 0.6523 (mmt) REVERT: D 89 ASN cc_start: 0.6942 (m-40) cc_final: 0.6675 (m-40) REVERT: E 26 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7078 (ptpp) REVERT: E 128 TYR cc_start: 0.8202 (m-80) cc_final: 0.7999 (m-80) REVERT: J 88 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.4471 (tpp) REVERT: Q 30 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7116 (ttpm) REVERT: Q 38 ILE cc_start: 0.7748 (pt) cc_final: 0.7547 (pt) REVERT: T 40 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: T 55 GLN cc_start: 0.5824 (OUTLIER) cc_final: 0.5447 (tt0) REVERT: f 17 MET cc_start: 0.6344 (mmm) cc_final: 0.6030 (mtp) REVERT: f 20 PHE cc_start: 0.7081 (m-80) cc_final: 0.6843 (m-80) REVERT: g 79 VAL cc_start: 0.5816 (OUTLIER) cc_final: 0.5541 (t) REVERT: g 124 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5652 (pm20) REVERT: g 176 LYS cc_start: 0.4501 (OUTLIER) cc_final: 0.4134 (mmmt) REVERT: h 1 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.3759 (ppp) REVERT: i 95 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6563 (mtm180) REVERT: j 1 MET cc_start: 0.7914 (ttm) cc_final: 0.7407 (ttm) REVERT: o 13 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6596 (ptm) REVERT: o 27 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: t 10 GLU cc_start: 0.6473 (tp30) cc_final: 0.6251 (tp30) REVERT: v 72 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7143 (pttm) REVERT: 3 18 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7723 (ttmt) REVERT: 4 1 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6406 (mtt) outliers start: 157 outliers final: 93 residues processed: 984 average time/residue: 2.2625 time to fit residues: 3136.9042 Evaluate side-chains 978 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 870 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 124 GLU Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 111 LYS Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 795 optimal weight: 2.9990 chunk 542 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 711 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 814 optimal weight: 10.0000 chunk 660 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 487 optimal weight: 30.0000 chunk 857 optimal weight: 0.1980 chunk 240 optimal weight: 0.9990 overall best weight: 4.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 109 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS I 4 ASN J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 40 GLN O 62 GLN T 13 GLN T 78 ASN U 9 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS ** 0 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 153876 Z= 0.250 Angle : 0.711 15.126 230273 Z= 0.382 Chirality : 0.039 0.371 29306 Planarity : 0.007 0.141 12254 Dihedral : 22.936 179.585 77146 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 4.22 % Allowed : 15.29 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.18 (0.11), residues: 5474 helix: 1.30 (0.12), residues: 1860 sheet: -0.09 (0.16), residues: 1064 loop : -0.61 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 42 HIS 0.009 0.001 HIS P 59 PHE 0.023 0.002 PHE F 8 TYR 0.018 0.002 TYR r 38 ARG 0.008 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 914 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6632 (mmp) cc_final: 0.6395 (mmm) REVERT: D 89 ASN cc_start: 0.6970 (m-40) cc_final: 0.6752 (m-40) REVERT: L 94 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7414 (mtm180) REVERT: L 111 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7395 (mptt) REVERT: Q 30 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7315 (ttpm) REVERT: Q 38 ILE cc_start: 0.7812 (pt) cc_final: 0.7558 (pt) REVERT: T 40 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5792 (tm-30) REVERT: c 5 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7200 (ptmm) REVERT: f 17 MET cc_start: 0.6396 (mmm) cc_final: 0.6123 (mtp) REVERT: f 20 PHE cc_start: 0.7087 (m-80) cc_final: 0.6857 (m-80) REVERT: g 176 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.3926 (mmmt) REVERT: h 1 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4046 (ppp) REVERT: i 95 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6485 (mtm180) REVERT: j 1 MET cc_start: 0.7869 (ttm) cc_final: 0.7356 (ttm) REVERT: j 106 GLU cc_start: 0.6728 (mp0) cc_final: 0.6456 (mp0) REVERT: n 46 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5919 (pp20) REVERT: o 27 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: t 7 ARG cc_start: 0.6496 (mtm180) cc_final: 0.6245 (mtm180) REVERT: t 10 GLU cc_start: 0.6494 (tp30) cc_final: 0.6275 (tp30) REVERT: v 72 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7114 (pttm) REVERT: 0 44 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6875 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7742 (ttmt) REVERT: 4 1 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6429 (mtt) outliers start: 193 outliers final: 119 residues processed: 1019 average time/residue: 2.2453 time to fit residues: 3226.7580 Evaluate side-chains 1022 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 889 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 26 ASN Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 0.5980 chunk 860 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 955 optimal weight: 0.6980 chunk 793 optimal weight: 5.9990 chunk 442 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 0.9980 chunk 501 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 146 ASN D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 40 GLN O 62 GLN T 13 GLN T 78 ASN c 251 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN l 88 ASN m 23 ASN s 28 ASN s 70 HIS ** 0 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 153876 Z= 0.166 Angle : 0.643 14.205 230273 Z= 0.355 Chirality : 0.036 0.391 29306 Planarity : 0.006 0.134 12254 Dihedral : 22.914 179.189 77146 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.94 % Allowed : 16.40 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 5474 helix: 1.46 (0.12), residues: 1869 sheet: -0.10 (0.16), residues: 1073 loop : -0.54 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 42 HIS 0.008 0.001 HIS P 59 PHE 0.023 0.001 PHE U 37 TYR 0.016 0.002 TYR r 38 ARG 0.008 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 908 time to evaluate : 5.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6640 (mmp) cc_final: 0.6428 (mmm) REVERT: D 89 ASN cc_start: 0.6968 (m-40) cc_final: 0.6736 (m-40) REVERT: E 14 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7118 (ttmp) REVERT: I 4 ASN cc_start: 0.4535 (OUTLIER) cc_final: 0.4293 (p0) REVERT: I 28 ILE cc_start: 0.7686 (mt) cc_final: 0.7401 (mp) REVERT: L 94 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7363 (mtm180) REVERT: L 111 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7123 (mptt) REVERT: Q 30 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7274 (ttpm) REVERT: Q 38 ILE cc_start: 0.7746 (pt) cc_final: 0.7513 (pt) REVERT: R 30 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7095 (mttm) REVERT: T 40 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5733 (tm-30) REVERT: T 55 GLN cc_start: 0.5908 (OUTLIER) cc_final: 0.5572 (tt0) REVERT: U 3 VAL cc_start: 0.6786 (OUTLIER) cc_final: 0.6468 (t) REVERT: c 72 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: f 17 MET cc_start: 0.6338 (mmm) cc_final: 0.6081 (mtp) REVERT: f 20 PHE cc_start: 0.7004 (m-80) cc_final: 0.6757 (m-80) REVERT: g 79 VAL cc_start: 0.5738 (OUTLIER) cc_final: 0.5487 (t) REVERT: g 124 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5615 (pm20) REVERT: h 1 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.3868 (ppp) REVERT: i 95 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6526 (mtm180) REVERT: m 74 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: n 46 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5878 (pp20) REVERT: r 69 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7481 (mp) REVERT: v 72 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7078 (pttm) REVERT: 0 44 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6862 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7704 (ttmt) REVERT: 4 1 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6434 (mtt) outliers start: 180 outliers final: 117 residues processed: 1003 average time/residue: 2.2393 time to fit residues: 3166.4776 Evaluate side-chains 1018 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 881 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 124 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 0.9990 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 0.0770 chunk 533 optimal weight: 10.0000 chunk 952 optimal weight: 1.9990 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 overall best weight: 4.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 109 GLN D 40 GLN D 116 GLN D 198 HIS E 70 ASN E 82 GLN F 11 HIS F 37 HIS J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 40 GLN O 62 GLN T 13 GLN T 78 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 153876 Z= 0.238 Angle : 0.698 14.994 230273 Z= 0.377 Chirality : 0.038 0.373 29306 Planarity : 0.007 0.140 12254 Dihedral : 22.918 179.536 77146 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 3.96 % Allowed : 16.97 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.11), residues: 5474 helix: 1.33 (0.12), residues: 1870 sheet: -0.09 (0.16), residues: 1059 loop : -0.61 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 42 HIS 0.010 0.001 HIS P 59 PHE 0.024 0.002 PHE F 8 TYR 0.018 0.002 TYR r 38 ARG 0.008 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 903 time to evaluate : 6.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6612 (mmp) cc_final: 0.6407 (mmm) REVERT: D 89 ASN cc_start: 0.6985 (m-40) cc_final: 0.6746 (m-40) REVERT: F 42 TRP cc_start: 0.6472 (m-10) cc_final: 0.6261 (m-10) REVERT: L 94 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7408 (mtm180) REVERT: L 111 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7400 (mptt) REVERT: Q 30 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7303 (ttpm) REVERT: Q 38 ILE cc_start: 0.7788 (pt) cc_final: 0.7544 (pt) REVERT: R 30 LYS cc_start: 0.7352 (mmmt) cc_final: 0.7110 (mttm) REVERT: T 40 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5782 (tm-30) REVERT: U 3 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6609 (t) REVERT: c 72 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: f 17 MET cc_start: 0.6364 (mmm) cc_final: 0.6075 (mtp) REVERT: f 20 PHE cc_start: 0.7034 (m-80) cc_final: 0.6795 (m-80) REVERT: g 176 LYS cc_start: 0.4438 (OUTLIER) cc_final: 0.4061 (mmmt) REVERT: i 95 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6506 (mtm180) REVERT: r 69 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7424 (mp) REVERT: t 46 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: v 72 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7105 (pttm) REVERT: w 70 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.5267 (mm-30) REVERT: 0 44 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6881 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7741 (ttmt) REVERT: 4 1 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6343 (mtt) outliers start: 181 outliers final: 126 residues processed: 999 average time/residue: 2.2499 time to fit residues: 3167.1961 Evaluate side-chains 1027 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 886 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 46 GLN Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain w residue 70 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 26 ASN Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 589 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 568 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 605 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 470 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 748 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 62 GLN T 13 GLN T 78 ASN g 104 ASN g 111 HIS ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS u 75 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 153876 Z= 0.422 Angle : 0.896 18.885 230273 Z= 0.459 Chirality : 0.047 0.430 29306 Planarity : 0.008 0.151 12254 Dihedral : 23.087 179.646 77146 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 4.18 % Allowed : 17.21 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.25 (0.11), residues: 5474 helix: 0.80 (0.12), residues: 1862 sheet: -0.29 (0.15), residues: 1077 loop : -0.77 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 42 HIS 0.013 0.002 HIS P 59 PHE 0.033 0.003 PHE F 8 TYR 0.025 0.003 TYR r 38 ARG 0.010 0.001 ARG c 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 895 time to evaluate : 6.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.6674 (mmp) cc_final: 0.6464 (mmm) REVERT: I 4 ASN cc_start: 0.5180 (OUTLIER) cc_final: 0.4835 (p0) REVERT: L 94 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7513 (mtm180) REVERT: f 20 PHE cc_start: 0.7181 (m-80) cc_final: 0.6975 (m-80) REVERT: h 1 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4671 (ppp) REVERT: i 95 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6379 (mtm180) REVERT: r 69 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7344 (mp) REVERT: t 46 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6299 (tm-30) REVERT: v 72 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7166 (pttm) REVERT: w 70 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.5231 (mm-30) REVERT: z 36 GLU cc_start: 0.7335 (pt0) cc_final: 0.6946 (pt0) REVERT: 0 44 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6842 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: 4 1 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6402 (mtt) outliers start: 191 outliers final: 133 residues processed: 1002 average time/residue: 2.2749 time to fit residues: 3199.0816 Evaluate side-chains 1024 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 880 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 113 ASP Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain i residue 140 LEU Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 46 GLN Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain w residue 70 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain 4 residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 866 optimal weight: 5.9990 chunk 912 optimal weight: 9.9990 chunk 832 optimal weight: 0.9980 chunk 887 optimal weight: 3.9990 chunk 534 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 696 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 801 optimal weight: 3.9990 chunk 839 optimal weight: 30.0000 chunk 884 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 116 GLN D 198 HIS E 122 ASN F 11 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 40 GLN O 62 GLN T 13 GLN T 75 HIS T 78 ASN c 251 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS u 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 153876 Z= 0.202 Angle : 0.677 14.389 230273 Z= 0.369 Chirality : 0.037 0.379 29306 Planarity : 0.007 0.136 12254 Dihedral : 22.924 179.285 77146 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 3.59 % Allowed : 18.29 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5474 helix: 1.26 (0.12), residues: 1869 sheet: -0.20 (0.15), residues: 1072 loop : -0.67 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 42 HIS 0.012 0.001 HIS P 59 PHE 0.021 0.002 PHE F 8 TYR 0.023 0.002 TYR I 6 ARG 0.008 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 904 time to evaluate : 5.378 Fit side-chains revert: symmetry clash REVERT: E 14 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7131 (ttmp) REVERT: L 94 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: M 57 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6588 (mpp80) REVERT: N 52 PRO cc_start: 0.6703 (Cg_endo) cc_final: 0.6468 (Cg_exo) REVERT: R 30 LYS cc_start: 0.7350 (mmmt) cc_final: 0.7113 (mttm) REVERT: T 55 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.5746 (tt0) REVERT: g 79 VAL cc_start: 0.5916 (OUTLIER) cc_final: 0.5593 (t) REVERT: g 176 LYS cc_start: 0.4439 (OUTLIER) cc_final: 0.4073 (mmmt) REVERT: i 95 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6463 (mtm180) REVERT: r 69 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7542 (mp) REVERT: v 72 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7087 (pttm) REVERT: w 70 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.5174 (mm-30) REVERT: z 36 GLU cc_start: 0.7254 (pt0) cc_final: 0.6910 (pt0) REVERT: 0 44 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6873 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: 4 1 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6289 (mtt) outliers start: 164 outliers final: 114 residues processed: 1001 average time/residue: 2.2740 time to fit residues: 3220.4329 Evaluate side-chains 1016 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 889 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 57 ARG Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 ASP Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain w residue 70 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 582 optimal weight: 10.9990 chunk 938 optimal weight: 9.9990 chunk 572 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 984 optimal weight: 10.0000 chunk 905 optimal weight: 1.9990 chunk 783 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN I 110 GLN J 64 GLN O 62 GLN T 13 GLN T 78 ASN g 104 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN ** j 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS u 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 153876 Z= 0.347 Angle : 0.814 16.842 230273 Z= 0.425 Chirality : 0.044 0.386 29306 Planarity : 0.008 0.147 12254 Dihedral : 23.013 179.970 77146 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 3.43 % Allowed : 18.66 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.14 (0.11), residues: 5474 helix: 0.96 (0.12), residues: 1862 sheet: -0.27 (0.15), residues: 1085 loop : -0.74 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 42 HIS 0.011 0.002 HIS P 59 PHE 0.028 0.003 PHE F 8 TYR 0.021 0.002 TYR r 38 ARG 0.009 0.001 ARG D 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 890 time to evaluate : 5.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7209 (ttmp) REVERT: L 94 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7461 (mtm180) REVERT: R 30 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7132 (mttm) REVERT: g 176 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3877 (mmmt) REVERT: h 1 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4675 (ppp) REVERT: i 95 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6413 (mtm180) REVERT: r 69 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7353 (mp) REVERT: v 72 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7145 (pttm) REVERT: w 70 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5240 (mm-30) REVERT: z 36 GLU cc_start: 0.7363 (pt0) cc_final: 0.6983 (pt0) REVERT: 0 44 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6846 (mtm-85) REVERT: 3 18 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7794 (ttmt) REVERT: 4 1 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6291 (mtt) outliers start: 157 outliers final: 125 residues processed: 985 average time/residue: 2.2385 time to fit residues: 3100.0980 Evaluate side-chains 1019 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 883 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 43 THR Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain g residue 176 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 ASP Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 41 LEU Chi-restraints excluded: chain t residue 83 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 72 LYS Chi-restraints excluded: chain w residue 7 VAL Chi-restraints excluded: chain w residue 70 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 27 SER Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 44 ARG Chi-restraints excluded: chain 0 residue 53 LYS Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 622 optimal weight: 10.0000 chunk 834 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 722 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 785 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 806 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 116 GLN D 198 HIS F 11 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN J 64 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 62 GLN T 13 GLN T 78 ASN g 104 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN m 23 ASN s 28 ASN s 70 HIS u 75 GLN ** u 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110573 restraints weight = 155502.530| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.71 r_work: 0.3166 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 153876 Z= 0.316 Angle : 0.787 16.276 230273 Z= 0.415 Chirality : 0.042 0.377 29306 Planarity : 0.008 0.145 12254 Dihedral : 23.011 179.881 77146 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 3.46 % Allowed : 18.85 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5474 helix: 0.94 (0.12), residues: 1857 sheet: -0.28 (0.15), residues: 1085 loop : -0.75 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 42 HIS 0.014 0.002 HIS T 75 PHE 0.027 0.002 PHE U 37 TYR 0.021 0.002 TYR D 76 ARG 0.008 0.001 ARG D 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46172.42 seconds wall clock time: 798 minutes 58.02 seconds (47938.02 seconds total)