Starting phenix.real_space_refine on Mon Mar 25 05:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6z_30598/03_2024/7d6z_30598.pdb" } resolution = 3.4 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= 1.000 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: 5 Type Number sf(0) Gaussians P 4758 5.49 5 S 159 5.16 5 C 74838 2.51 5 N 27705 2.21 5 O 41403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 8": "OE1" <-> "OE2" Residue "1 GLU 44": "OE1" <-> "OE2" Residue "6 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 11": "NH1" <-> "NH2" Residue "T ARG 30": "NH1" <-> "NH2" Residue "T ARG 45": "NH1" <-> "NH2" Residue "T PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 3": "NH1" <-> "NH2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b GLU 7": "OE1" <-> "OE2" Residue "b PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 32": "OE1" <-> "OE2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "g GLU 1011": "OE1" <-> "OE2" Residue "g GLU 1021": "OE1" <-> "OE2" Residue "g GLU 1064": "OE1" <-> "OE2" Residue "g GLU 1088": "OE1" <-> "OE2" Residue "g GLU 1095": "OE1" <-> "OE2" Residue "g GLU 1121": "OE1" <-> "OE2" Residue "h GLU 31": "OE1" <-> "OE2" Residue "h GLU 82": "OE1" <-> "OE2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h GLU 108": "OE1" <-> "OE2" Residue "i TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 52": "OE1" <-> "OE2" Residue "i GLU 56": "OE1" <-> "OE2" Residue "i ASP 88": "OD1" <-> "OD2" Residue "i GLU 145": "OE1" <-> "OE2" Residue "j GLU 82": "OE1" <-> "OE2" Residue "j ARG 131": "NH1" <-> "NH2" Residue "j GLU 161": "OE1" <-> "OE2" Residue "j GLU 166": "OE1" <-> "OE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "k GLU 160": "OE1" <-> "OE2" Residue "k GLU 202": "OE1" <-> "OE2" Residue "m PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 23": "OE1" <-> "OE2" Residue "m GLU 69": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m GLU 98": "OE1" <-> "OE2" Residue "n GLU 90": "OE1" <-> "OE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "n GLU 146": "OE1" <-> "OE2" Residue "o GLU 42": "OE1" <-> "OE2" Residue "o GLU 47": "OE1" <-> "OE2" Residue "o GLU 52": "OE1" <-> "OE2" Residue "p ARG 124": "NH1" <-> "NH2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "s ARG 56": "NH1" <-> "NH2" Residue "u GLU 92": "OE1" <-> "OE2" Residue "v GLU 14": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 28": "NH1" <-> "NH2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 48": "OE1" <-> "OE2" Residue "x GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148863 Number of models: 1 Model: "" Number of chains: 58 Chain: "0" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "1" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "2" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1392 Classifications: {'RNA': 65} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 25} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain breaks: 6 Chain: "3" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1496 Classifications: {'RNA': 70} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 9, 'rna3p': 60} Chain breaks: 6 Chain: "4" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1406 Classifications: {'RNA': 66} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 56} Chain breaks: 7 Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 280, 'rna2p_pyr': 149, 'rna3p_pur': 1394, 'rna3p_pyr': 1080} Link IDs: {'rna2p': 429, 'rna3p': 2473} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} 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: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 359 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" 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: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: "X" 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: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 764 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "a" 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: "b" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "c" 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: "d" 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: "e" 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: "f" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 88, 'rna3p_pur': 755, 'rna3p_pyr': 577} Link IDs: {'rna2p': 207, 'rna3p': 1331} Chain: "g" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1346 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 160} Chain: "h" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "i" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "j" 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: "k" 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: "l" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "m" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "n" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "o" 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: "p" 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: "q" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "r" 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: "s" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "t" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "u" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "v" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "w" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "x" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "z" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Time building chain proxies: 57.97, per 1000 atoms: 0.39 Number of scatterers: 148863 At special positions: 0 Unit cell: (313.26, 271.86, 226.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 159 16.00 P 4758 15.00 O 41403 8.00 N 27705 7.00 C 74838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.15 Conformation dependent library (CDL) restraints added in 7.5 seconds 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10974 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 80 sheets defined 30.3% alpha, 15.0% beta 1359 base pairs and 2724 stacking pairs defined. Time for finding SS restraints: 53.31 Creating SS restraints... Processing helix chain '0' and resid 6 through 41 removed outlier: 3.707A pdb=" N ARG 0 10 " --> pdb=" O SER 0 6 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU 0 15 " --> pdb=" O ALA 0 11 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS 0 16 " --> pdb=" O ILE 0 12 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE 0 32 " --> pdb=" O MET 0 28 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL 0 35 " --> pdb=" O PHE 0 31 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 65 Proline residue: 0 56 - end of helix removed outlier: 3.753A pdb=" N ASP 0 59 " --> pdb=" O GLN 0 55 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA 0 63 " --> pdb=" O ASP 0 59 " (cutoff:3.500A) Processing helix chain '0' and resid 69 through 84 removed outlier: 3.551A pdb=" N ARG 0 74 " --> pdb=" O ASN 0 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS 0 76 " --> pdb=" O ALA 0 72 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN 0 82 " --> pdb=" O ASN 0 78 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN 0 84 " --> pdb=" O THR 0 80 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 44 through 51 Processing helix chain '6' and resid 56 through 62 removed outlier: 4.354A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.521A pdb=" N LEU C 202 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 208 through 213 removed outlier: 4.020A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.716A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.719A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.791A pdb=" N SER E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.679A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.224A pdb=" N ILE E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.962A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 200 removed outlier: 3.504A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.560A pdb=" N ASP F 10 " --> pdb=" O ASP F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 21 removed outlier: 3.563A pdb=" N MET F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.914A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 removed outlier: 3.792A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.796A pdb=" N TRP F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.631A pdb=" N ILE F 111 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 4.030A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.618A pdb=" N LEU F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 74 removed outlier: 3.910A pdb=" N GLY G 66 " --> pdb=" O TRP G 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 30 through 34 removed outlier: 4.012A pdb=" N GLY H 34 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 30 removed outlier: 3.867A pdb=" N ALA I 27 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 28 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN I 30 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 Processing helix chain 'I' and resid 92 through 96 removed outlier: 4.006A pdb=" N ASP I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 129 through 135 removed outlier: 4.057A pdb=" N ALA I 133 " --> pdb=" O ILE I 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 36 removed outlier: 4.373A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.696A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 4.552A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.623A pdb=" N GLY J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA J 117 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.705A pdb=" N LEU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG K 108 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 108' Processing helix chain 'K' and resid 112 through 118 removed outlier: 3.670A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 136 removed outlier: 3.893A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.639A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 removed outlier: 3.861A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 32 removed outlier: 3.781A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.523A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.623A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.729A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.757A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 21 removed outlier: 3.500A pdb=" N GLN O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 85 removed outlier: 3.608A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 113 removed outlier: 3.592A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.914A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 57 removed outlier: 3.695A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER P 57 " --> pdb=" O GLY P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 57' Processing helix chain 'P' and resid 97 through 102 removed outlier: 3.508A pdb=" N GLU P 102 " --> pdb=" O TYR P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 109 removed outlier: 3.516A pdb=" N ALA P 107 " --> pdb=" O THR P 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA P 108 " --> pdb=" O GLY P 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG P 109 " --> pdb=" O LYS P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 104 through 109' Processing helix chain 'Q' and resid 11 through 18 removed outlier: 3.532A pdb=" N LEU Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.528A pdb=" N ARG Q 28 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 29' Processing helix chain 'Q' and resid 31 through 48 removed outlier: 4.071A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 57 removed outlier: 3.691A pdb=" N GLN Q 52 " --> pdb=" O ARG Q 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 70 removed outlier: 3.743A pdb=" N ALA Q 63 " --> pdb=" O GLN Q 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 removed outlier: 4.019A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.664A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.623A pdb=" N THR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA Q 108 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 21 removed outlier: 3.588A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 3.907A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 47 removed outlier: 3.569A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 61 removed outlier: 3.790A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.934A pdb=" N GLY S 91 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 28 removed outlier: 3.597A pdb=" N THR T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 51 removed outlier: 3.565A pdb=" N GLY T 46 " --> pdb=" O PRO T 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 21 removed outlier: 3.532A pdb=" N LEU V 20 " --> pdb=" O ALA V 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG V 21 " --> pdb=" O SER V 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 16 through 21' Processing helix chain 'V' and resid 44 through 49 Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.084A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 63 removed outlier: 3.807A pdb=" N LYS X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.628A pdb=" N GLU X 70 " --> pdb=" O THR X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 8 removed outlier: 3.942A pdb=" N ARG Y 7 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 22 removed outlier: 4.072A pdb=" N LEU Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 34 removed outlier: 3.632A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 60 removed outlier: 3.671A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS Y 54 " --> pdb=" O VAL Y 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 27 removed outlier: 3.620A pdb=" N SER Z 21 " --> pdb=" O SER Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 51 removed outlier: 3.653A pdb=" N LYS Z 44 " --> pdb=" O LYS Z 40 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS Z 49 " --> pdb=" O ALA Z 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 17 removed outlier: 3.591A pdb=" N ARG a 17 " --> pdb=" O ARG a 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 17 removed outlier: 4.073A pdb=" N SER c 15 " --> pdb=" O LYS c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 37 through 43 removed outlier: 3.620A pdb=" N HIS d 43 " --> pdb=" O LYS d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 54 No H-bonds generated for 'chain 'd' and resid 52 through 54' Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.611A pdb=" N ALA d 60 " --> pdb=" O GLY d 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 33 Processing helix chain 'g' and resid 1026 through 1032 removed outlier: 4.142A pdb=" N ASP g1032 " --> pdb=" O GLN g1028 " (cutoff:3.500A) Processing helix chain 'g' and resid 1034 through 1041 removed outlier: 3.800A pdb=" N GLU g1041 " --> pdb=" O THR g1037 " (cutoff:3.500A) Processing helix chain 'g' and resid 1048 through 1052 removed outlier: 3.601A pdb=" N VAL g1051 " --> pdb=" O ALA g1048 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP g1052 " --> pdb=" O THR g1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 1048 through 1052' Processing helix chain 'g' and resid 1126 through 1139 removed outlier: 3.975A pdb=" N ILE g1130 " --> pdb=" O LEU g1126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP g1135 " --> pdb=" O GLN g1131 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS g1136 " --> pdb=" O HIS g1132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU g1137 " --> pdb=" O GLU g1133 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL g1138 " --> pdb=" O MET g1134 " (cutoff:3.500A) Processing helix chain 'g' and resid 1141 through 1146 removed outlier: 3.606A pdb=" N TYR g1145 " --> pdb=" O PHE g1142 " (cutoff:3.500A) Processing helix chain 'g' and resid 1149 through 1154 Processing helix chain 'g' and resid 1155 through 1163 removed outlier: 3.925A pdb=" N GLU g1159 " --> pdb=" O ARG g1155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS g1160 " --> pdb=" O GLN g1156 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU g1161 " --> pdb=" O LYS g1157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG g1163 " --> pdb=" O GLU g1159 " (cutoff:3.500A) Processing helix chain 'g' and resid 1164 through 1166 No H-bonds generated for 'chain 'g' and resid 1164 through 1166' Processing helix chain 'h' and resid 20 through 25 removed outlier: 3.937A pdb=" N ILE h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU h 25 " --> pdb=" O ALA h 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 20 through 25' Processing helix chain 'h' and resid 27 through 33 Processing helix chain 'h' and resid 50 through 59 removed outlier: 3.800A pdb=" N VAL h 54 " --> pdb=" O PRO h 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG h 57 " --> pdb=" O ILE h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 70 removed outlier: 3.542A pdb=" N ASP h 69 " --> pdb=" O ASP h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 77 removed outlier: 3.513A pdb=" N ILE h 76 " --> pdb=" O ARG h 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 31 removed outlier: 3.525A pdb=" N LYS i 28 " --> pdb=" O PRO i 25 " (cutoff:3.500A) Proline residue: i 29 - end of helix Processing helix chain 'i' and resid 42 through 63 removed outlier: 3.911A pdb=" N VAL i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Proline residue: i 48 - end of helix removed outlier: 3.690A pdb=" N LYS i 59 " --> pdb=" O ALA i 55 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE i 60 " --> pdb=" O GLU i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 73 through 77 removed outlier: 3.719A pdb=" N SER i 77 " --> pdb=" O ARG i 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 86 Processing helix chain 'i' and resid 103 through 118 removed outlier: 3.737A pdb=" N VAL i 107 " --> pdb=" O ASN i 103 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN i 109 " --> pdb=" O LYS i 105 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER i 110 " --> pdb=" O THR i 106 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE i 111 " --> pdb=" O VAL i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 118 through 123 removed outlier: 4.083A pdb=" N GLN i 122 " --> pdb=" O GLU i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 142 through 147 removed outlier: 3.868A pdb=" N ASN i 146 " --> pdb=" O GLU i 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER i 147 " --> pdb=" O LYS i 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 142 through 147' Processing helix chain 'i' and resid 149 through 154 removed outlier: 3.677A pdb=" N ASP i 153 " --> pdb=" O GLY i 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 180 Processing helix chain 'i' and resid 206 through 223 removed outlier: 3.805A pdb=" N THR i 211 " --> pdb=" O ILE i 207 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU i 212 " --> pdb=" O ARG i 208 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR i 213 " --> pdb=" O ALA i 209 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 47 removed outlier: 3.948A pdb=" N GLN j 41 " --> pdb=" O PHE j 37 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR j 44 " --> pdb=" O ARG j 40 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS j 45 " --> pdb=" O GLN j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 72 through 78 removed outlier: 3.749A pdb=" N VAL j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 96 removed outlier: 3.756A pdb=" N LEU j 87 " --> pdb=" O ASP j 83 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS j 89 " --> pdb=" O GLU j 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL j 90 " --> pdb=" O LYS j 86 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 126 removed outlier: 4.207A pdb=" N GLN j 123 " --> pdb=" O SER j 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG j 126 " --> pdb=" O SER j 122 " (cutoff:3.500A) Processing helix chain 'j' and resid 129 through 142 removed outlier: 3.551A pdb=" N ALA j 141 " --> pdb=" O ALA j 137 " (cutoff:3.500A) Processing helix chain 'j' and resid 156 through 160 removed outlier: 3.687A pdb=" N GLY j 159 " --> pdb=" O ARG j 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA j 160 " --> pdb=" O LEU j 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 156 through 160' Processing helix chain 'k' and resid 49 through 66 removed outlier: 4.086A pdb=" N GLU k 57 " --> pdb=" O VAL k 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS k 58 " --> pdb=" O GLN k 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL k 61 " --> pdb=" O GLU k 57 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR k 65 " --> pdb=" O VAL k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 82 Processing helix chain 'k' and resid 87 through 92 removed outlier: 3.704A pdb=" N LEU k 91 " --> pdb=" O GLY k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 105 Processing helix chain 'k' and resid 111 through 116 Processing helix chain 'k' and resid 160 through 165 removed outlier: 3.517A pdb=" N GLN k 164 " --> pdb=" O GLU k 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 197 through 202 removed outlier: 4.132A pdb=" N VAL k 201 " --> pdb=" O GLU k 197 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 69 removed outlier: 3.631A pdb=" N LYS l 62 " --> pdb=" O ALA l 58 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG l 69 " --> pdb=" O GLU l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 112 through 117 removed outlier: 3.865A pdb=" N VAL l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 137 Processing helix chain 'l' and resid 140 through 145 Processing helix chain 'l' and resid 149 through 154 Processing helix chain 'l' and resid 155 through 158 removed outlier: 4.169A pdb=" N GLY l 158 " --> pdb=" O ALA l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 155 through 158' Processing helix chain 'm' and resid 17 through 32 removed outlier: 3.972A pdb=" N ALA m 28 " --> pdb=" O ARG m 24 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA m 32 " --> pdb=" O ALA m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 81 removed outlier: 3.711A pdb=" N ASP m 72 " --> pdb=" O GLN m 68 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU m 73 " --> pdb=" O GLU m 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 20 through 31 removed outlier: 4.057A pdb=" N ASN n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 35 through 49 removed outlier: 3.631A pdb=" N SER n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR n 49 " --> pdb=" O SER n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 59 through 65 removed outlier: 3.631A pdb=" N ALA n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 109 removed outlier: 3.725A pdb=" N ASN n 97 " --> pdb=" O PRO n 93 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA n 98 " --> pdb=" O VAL n 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG n 102 " --> pdb=" O ALA n 98 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL n 105 " --> pdb=" O MET n 101 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 129 removed outlier: 3.647A pdb=" N ALA n 121 " --> pdb=" O ALA n 117 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU n 129 " --> pdb=" O SER n 125 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 145 removed outlier: 3.607A pdb=" N ARG n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 20 Processing helix chain 'o' and resid 32 through 43 removed outlier: 3.873A pdb=" N VAL o 39 " --> pdb=" O ALA o 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 92 removed outlier: 3.946A pdb=" N LEU o 92 " --> pdb=" O LYS o 89 " (cutoff:3.500A) Processing helix chain 'o' and resid 95 through 99 Processing helix chain 'o' and resid 112 through 120 removed outlier: 3.536A pdb=" N ARG o 117 " --> pdb=" O ASP o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 35 through 39 Processing helix chain 'p' and resid 49 through 53 removed outlier: 3.616A pdb=" N GLU p 53 " --> pdb=" O GLN p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 87 removed outlier: 3.846A pdb=" N ARG p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 90 through 95 removed outlier: 3.538A pdb=" N LEU p 94 " --> pdb=" O TYR p 90 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG p 95 " --> pdb=" O ASP p 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 90 through 95' Processing helix chain 'p' and resid 95 through 100 removed outlier: 4.344A pdb=" N LYS p 100 " --> pdb=" O SER p 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 33 removed outlier: 3.572A pdb=" N THR q 32 " --> pdb=" O THR q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 88 removed outlier: 3.719A pdb=" N ASP q 85 " --> pdb=" O GLU q 81 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA q 86 " --> pdb=" O LYS q 82 " (cutoff:3.500A) Processing helix chain 'r' and resid 59 through 72 removed outlier: 3.542A pdb=" N GLN r 64 " --> pdb=" O PRO r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 94 through 102 removed outlier: 3.944A pdb=" N LEU r 100 " --> pdb=" O THR r 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN r 101 " --> pdb=" O ILE r 97 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 113 through 117 removed outlier: 3.522A pdb=" N LYS s 116 " --> pdb=" O ALA s 113 " (cutoff:3.500A) Processing helix chain 't' and resid 14 through 19 removed outlier: 3.671A pdb=" N LEU t 19 " --> pdb=" O ALA t 15 " (cutoff:3.500A) Processing helix chain 't' and resid 20 through 22 No H-bonds generated for 'chain 't' and resid 20 through 22' Processing helix chain 't' and resid 26 through 34 removed outlier: 3.669A pdb=" N LEU t 34 " --> pdb=" O SER t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 61 removed outlier: 4.269A pdb=" N THR t 55 " --> pdb=" O GLY t 51 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU t 56 " --> pdb=" O GLN t 52 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU t 59 " --> pdb=" O THR t 55 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 3.736A pdb=" N GLU t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP t 82 " --> pdb=" O LYS t 78 " (cutoff:3.500A) Processing helix chain 't' and resid 85 through 94 Processing helix chain 'u' and resid 3 through 20 removed outlier: 3.660A pdb=" N LYS u 7 " --> pdb=" O LYS u 3 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL u 11 " --> pdb=" O LYS u 7 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS u 12 " --> pdb=" O ALA u 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG u 13 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA u 17 " --> pdb=" O ARG u 13 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP u 18 " --> pdb=" O VAL u 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR u 20 " --> pdb=" O LEU u 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 25 through 30 removed outlier: 3.709A pdb=" N ILE u 30 " --> pdb=" O GLU u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 56 through 60 removed outlier: 3.553A pdb=" N ARG u 59 " --> pdb=" O SER u 56 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN u 60 " --> pdb=" O PRO u 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 56 through 60' Processing helix chain 'u' and resid 81 through 89 removed outlier: 3.703A pdb=" N ARG u 85 " --> pdb=" O ARG u 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET u 89 " --> pdb=" O ARG u 85 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 15 removed outlier: 3.927A pdb=" N ILE v 11 " --> pdb=" O ALA v 7 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER v 13 " --> pdb=" O ALA v 9 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 44 removed outlier: 3.683A pdb=" N HIS v 38 " --> pdb=" O ALA v 34 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY v 41 " --> pdb=" O ASN v 37 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS v 42 " --> pdb=" O HIS v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 72 removed outlier: 3.696A pdb=" N GLY v 55 " --> pdb=" O HIS v 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS v 65 " --> pdb=" O SER v 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG v 72 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 74 through 86 removed outlier: 3.749A pdb=" N GLU v 83 " --> pdb=" O THR v 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG v 84 " --> pdb=" O GLN v 80 " (cutoff:3.500A) Processing helix chain 'w' and resid 54 through 63 removed outlier: 3.540A pdb=" N GLY w 62 " --> pdb=" O ALA w 58 " (cutoff:3.500A) Processing helix chain 'w' and resid 68 through 76 removed outlier: 3.715A pdb=" N LYS w 76 " --> pdb=" O ALA w 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 49 through 63 removed outlier: 3.748A pdb=" N ARG y 53 " --> pdb=" O ALA y 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN y 54 " --> pdb=" O LYS y 50 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU y 55 " --> pdb=" O TYR y 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE y 59 " --> pdb=" O LEU y 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 12 through 17 Processing helix chain 'z' and resid 19 through 24 removed outlier: 3.779A pdb=" N GLU z 24 " --> pdb=" O GLU z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 41 through 45 removed outlier: 3.580A pdb=" N ILE z 45 " --> pdb=" O PRO z 42 " (cutoff:3.500A) Processing helix chain 'z' and resid 63 through 67 removed outlier: 3.761A pdb=" N MET z 66 " --> pdb=" O THR z 63 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL z 67 " --> pdb=" O ASP z 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 63 through 67' Processing helix chain 'z' and resid 70 through 75 removed outlier: 4.005A pdb=" N PHE z 74 " --> pdb=" O LEU z 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '6' and resid 21 through 25 removed outlier: 3.848A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER 6 15 " --> pdb=" O LEU 6 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.529A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.707A pdb=" N LEU C 130 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG C 189 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL C 144 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET C 181 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 15 removed outlier: 6.747A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.607A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.754A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB2, first strand: chain 'F' and resid 90 through 92 removed outlier: 6.899A pdb=" N THR F 157 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE F 34 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.529A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL G 23 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 127 removed outlier: 7.126A pdb=" N GLU G 130 " --> pdb=" O PRO G 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.734A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AB9, first strand: chain 'H' and resid 8 through 9 removed outlier: 3.600A pdb=" N VAL H 9 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 13 " --> pdb=" O VAL H 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.766A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC3, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.909A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.608A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 76 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA P 58 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE P 50 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE P 64 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N GLU P 44 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU P 27 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL P 86 " --> pdb=" O GLU P 27 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS P 29 " --> pdb=" O ILE P 84 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE P 84 " --> pdb=" O LYS P 29 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP P 31 " --> pdb=" O ASP P 82 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASP P 82 " --> pdb=" O TRP P 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.715A pdb=" N ALA L 75 " --> pdb=" O LYS L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.808A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.386A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 40 through 41 Processing sheet with id=AC9, first strand: chain 'M' and resid 72 through 75 removed outlier: 3.636A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 33 through 37 Processing sheet with id=AD2, first strand: chain 'O' and resid 47 through 49 removed outlier: 3.737A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 29 through 30 Processing sheet with id=AD4, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.664A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.569A pdb=" N THR R 94 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AD7, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.676A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 82 through 85 Processing sheet with id=AD9, first strand: chain 'T' and resid 35 through 37 Processing sheet with id=AE1, first strand: chain 'U' and resid 65 through 66 removed outlier: 6.624A pdb=" N LYS U 33 " --> pdb=" O VAL U 28 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL U 28 " --> pdb=" O LYS U 33 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE U 35 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 44 through 45 Processing sheet with id=AE3, first strand: chain 'U' and resid 83 through 84 Processing sheet with id=AE4, first strand: chain 'V' and resid 68 through 70 removed outlier: 6.546A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 22 through 23 removed outlier: 3.609A pdb=" N VAL W 38 " --> pdb=" O LEU W 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'X' and resid 13 through 16 Processing sheet with id=AE8, first strand: chain 'X' and resid 34 through 39 Processing sheet with id=AE9, first strand: chain 'Z' and resid 29 through 30 removed outlier: 6.987A pdb=" N THR Z 86 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 33 through 34 removed outlier: 4.026A pdb=" N LYS Z 81 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 67 through 70 removed outlier: 3.685A pdb=" N ARG Z 73 " --> pdb=" O HIS Z 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 29 through 30 Processing sheet with id=AF4, first strand: chain 'a' and resid 48 through 49 removed outlier: 3.526A pdb=" N ARG a 52 " --> pdb=" O TYR a 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 20 through 25 removed outlier: 3.587A pdb=" N THR b 23 " --> pdb=" O ILE b 9 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 15 through 16 Processing sheet with id=AF7, first strand: chain 'e' and resid 2 through 3 Processing sheet with id=AF8, first strand: chain 'e' and resid 14 through 18 Processing sheet with id=AF9, first strand: chain 'g' and resid 1045 through 1046 removed outlier: 6.672A pdb=" N ARG g1109 " --> pdb=" O PRO g1075 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU g1077 " --> pdb=" O LYS g1107 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS g1107 " --> pdb=" O LEU g1077 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU g1079 " --> pdb=" O LYS g1105 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS g1105 " --> pdb=" O GLU g1079 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL g1106 " --> pdb=" O ALA g1122 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA g1122 " --> pdb=" O VAL g1106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 1084 through 1088 removed outlier: 4.089A pdb=" N ILE g1086 " --> pdb=" O VAL g1100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL g1100 " --> pdb=" O ILE g1086 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA g1098 " --> pdb=" O GLU g1088 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 4 through 6 removed outlier: 3.869A pdb=" N SER h 4 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU h 6 " --> pdb=" O ARG h 14 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE h 17 " --> pdb=" O TYR h 105 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR h 105 " --> pdb=" O ILE h 17 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE h 19 " --> pdb=" O PHE h 103 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE h 103 " --> pdb=" O ILE h 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 4 through 6 removed outlier: 3.869A pdb=" N SER h 4 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU h 6 " --> pdb=" O ARG h 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG h 13 " --> pdb=" O PHE h 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE h 109 " --> pdb=" O ARG h 13 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 91 through 92 removed outlier: 6.522A pdb=" N PHE i 69 " --> pdb=" O VAL i 92 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL i 163 " --> pdb=" O ILE i 186 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 52 through 56 removed outlier: 6.814A pdb=" N HIS j 69 " --> pdb=" O SER j 53 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE j 55 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR j 67 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE j 64 " --> pdb=" O GLN j 100 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASN j 102 " --> pdb=" O ILE j 64 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL j 66 " --> pdb=" O ASN j 102 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA j 104 " --> pdb=" O VAL j 66 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE j 68 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'j' and resid 168 through 171 removed outlier: 4.000A pdb=" N ILE j 149 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 123 through 125 Processing sheet with id=AG8, first strand: chain 'l' and resid 14 through 15 Processing sheet with id=AG9, first strand: chain 'l' and resid 20 through 21 Processing sheet with id=AH1, first strand: chain 'l' and resid 85 through 88 Processing sheet with id=AH2, first strand: chain 'm' and resid 2 through 3 Processing sheet with id=AH3, first strand: chain 'm' and resid 40 through 44 removed outlier: 5.953A pdb=" N TYR m 59 " --> pdb=" O TRP m 42 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL m 7 " --> pdb=" O SER m 87 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER m 87 " --> pdb=" O VAL m 7 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 73 through 76 Processing sheet with id=AH5, first strand: chain 'o' and resid 24 through 25 removed outlier: 6.683A pdb=" N GLU o 60 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE o 49 " --> pdb=" O GLU o 60 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR o 62 " --> pdb=" O GLU o 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'o' and resid 86 through 87 Processing sheet with id=AH7, first strand: chain 'p' and resid 6 through 8 removed outlier: 3.604A pdb=" N LYS p 22 " --> pdb=" O ASP p 62 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL p 29 " --> pdb=" O ILE p 65 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL p 67 " --> pdb=" O VAL p 29 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 45 through 48 removed outlier: 3.677A pdb=" N ARG q 45 " --> pdb=" O THR q 69 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 45 through 48 removed outlier: 3.677A pdb=" N ARG q 45 " --> pdb=" O THR q 69 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 51 through 52 Processing sheet with id=AI2, first strand: chain 'r' and resid 43 through 46 removed outlier: 6.582A pdb=" N LEU r 82 " --> pdb=" O ILE r 107 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN r 109 " --> pdb=" O LEU r 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL r 86 " --> pdb=" O THR r 111 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 's' and resid 30 through 31 Processing sheet with id=AI4, first strand: chain 's' and resid 36 through 37 removed outlier: 3.507A pdb=" N ARG s 36 " --> pdb=" O ARG s 54 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR s 95 " --> pdb=" O THR s 64 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'u' and resid 73 through 74 removed outlier: 3.749A pdb=" N LEU u 79 " --> pdb=" O LEU u 74 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'w' and resid 32 through 35 removed outlier: 6.915A pdb=" N PHE w 32 " --> pdb=" O ASP w 23 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP w 23 " --> pdb=" O PHE w 32 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU w 34 " --> pdb=" O VAL w 21 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL w 2 " --> pdb=" O THR w 66 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'x' and resid 8 through 14 removed outlier: 7.141A pdb=" N GLN x 9 " --> pdb=" O GLU x 26 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU x 26 " --> pdb=" O GLN x 9 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL x 22 " --> pdb=" O VAL x 13 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TRP x 73 " --> pdb=" O HIS x 45 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU x 75 " --> pdb=" O HIS x 47 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU x 60 " --> pdb=" O VAL x 76 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL x 78 " --> pdb=" O VAL x 58 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL x 58 " --> pdb=" O VAL x 78 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'z' and resid 48 through 52 1294 hydrogen bonds defined for protein. 3519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3337 hydrogen bonds 5396 hydrogen bond angles 0 basepair planarities 1359 basepair parallelities 2724 stacking parallelities Total time for adding SS restraints: 269.71 Time building geometry restraints manager: 66.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 17713 1.32 - 1.45: 69196 1.45 - 1.57: 65042 1.57 - 1.69: 9494 1.69 - 1.81: 284 Bond restraints: 161729 Sorted by residual: bond pdb=" C THR D 151 " pdb=" N PRO D 152 " ideal model delta sigma weight residual 1.334 1.274 0.060 2.34e-02 1.83e+03 6.47e+00 bond pdb=" CB VAL C 195 " pdb=" CG1 VAL C 195 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB VAL C 220 " pdb=" CG2 VAL C 220 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CB ILE L 111 " pdb=" CG2 ILE L 111 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CB VAL C 141 " pdb=" CG1 VAL C 141 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.86e+00 ... (remaining 161724 not shown) Histogram of bond angle deviations from ideal: 97.05 - 105.11: 22268 105.11 - 113.16: 98818 113.16 - 121.22: 78207 121.22 - 129.28: 39312 129.28 - 137.34: 3288 Bond angle restraints: 241893 Sorted by residual: angle pdb=" C PHE 1 37 " pdb=" N TYR 1 38 " pdb=" CA TYR 1 38 " ideal model delta sigma weight residual 121.54 134.36 -12.82 1.91e+00 2.74e-01 4.50e+01 angle pdb=" N ILE d 32 " pdb=" CA ILE d 32 " pdb=" C ILE d 32 " ideal model delta sigma weight residual 109.34 122.58 -13.24 2.08e+00 2.31e-01 4.05e+01 angle pdb=" CA LEU m 54 " pdb=" CB LEU m 54 " pdb=" CG LEU m 54 " ideal model delta sigma weight residual 116.30 136.46 -20.16 3.50e+00 8.16e-02 3.32e+01 angle pdb=" N VAL K 35 " pdb=" CA VAL K 35 " pdb=" C VAL K 35 " ideal model delta sigma weight residual 113.20 107.88 5.32 9.60e-01 1.09e+00 3.07e+01 angle pdb=" C GLU 1 24 " pdb=" N LYS 1 25 " pdb=" CA LYS 1 25 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.96e+01 ... (remaining 241888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 91989 35.84 - 71.68: 10315 71.68 - 107.53: 1313 107.53 - 143.37: 8 143.37 - 179.21: 26 Dihedral angle restraints: 103651 sinusoidal: 86642 harmonic: 17009 Sorted by residual: dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -100.31 -79.69 0 5.00e+00 4.00e-02 2.54e+02 dihedral pdb=" CA GLU K 92 " pdb=" C GLU K 92 " pdb=" N GLN K 93 " pdb=" CA GLN K 93 " ideal model delta harmonic sigma weight residual -180.00 -112.67 -67.33 0 5.00e+00 4.00e-02 1.81e+02 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 -113.50 -66.50 0 5.00e+00 4.00e-02 1.77e+02 ... (remaining 103648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 27943 0.069 - 0.137: 2668 0.137 - 0.206: 262 0.206 - 0.275: 42 0.275 - 0.344: 13 Chirality restraints: 30928 Sorted by residual: chirality pdb=" C3' U f 96 " pdb=" C4' U f 96 " pdb=" O3' U f 96 " pdb=" C2' U f 96 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C3' G f 115 " pdb=" C4' G f 115 " pdb=" O3' G f 115 " pdb=" C2' G f 115 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' A f1201 " pdb=" C4' A f1201 " pdb=" O3' A f1201 " pdb=" C2' A f1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 30925 not shown) Planarity restraints: 12967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.083 5.00e-02 4.00e+02 1.25e-01 2.48e+01 pdb=" N PRO D 152 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 57 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C VAL M 57 " 0.068 2.00e-02 2.50e+03 pdb=" O VAL M 57 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS M 58 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER k 138 " -0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO k 139 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO k 139 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO k 139 " -0.050 5.00e-02 4.00e+02 ... (remaining 12964 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 423 2.43 - 3.05: 80107 3.05 - 3.67: 258126 3.67 - 4.28: 412334 4.28 - 4.90: 580740 Nonbonded interactions: 1331730 Sorted by model distance: nonbonded pdb=" CD1 LEU Y 21 " pdb=" OE2 GLU Z 5 " model vdw 1.815 3.460 nonbonded pdb=" O6 G f 64 " pdb=" N6 A f 101 " model vdw 2.187 2.520 nonbonded pdb=" O2' G A 370 " pdb=" OP1 G A 424 " model vdw 2.218 2.440 nonbonded pdb=" O2' G A1337 " pdb=" O ASP h 42 " model vdw 2.232 2.440 nonbonded pdb=" O2' U f 662 " pdb=" OP1 G f 836 " model vdw 2.236 2.440 ... (remaining 1331725 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 13.350 Check model and map are aligned: 1.630 Set scattering table: 1.050 Process input model: 552.910 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 576.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 : 0.007 0.081 161729 Z= 0.424 Angle : 0.769 20.161 241893 Z= 0.399 Chirality : 0.043 0.344 30928 Planarity : 0.006 0.125 12967 Dihedral : 22.664 179.209 92674 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.98 % Favored : 89.61 % Rotamer: Outliers : 0.39 % Allowed : 10.11 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.40 % 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: -5.33 (0.08), residues: 5864 helix: -4.78 (0.04), residues: 1668 sheet: -2.79 (0.14), residues: 1131 loop : -3.09 (0.09), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 213 HIS 0.010 0.002 HIS N 16 PHE 0.021 0.002 PHE p 127 TYR 0.023 0.002 TYR i 22 ARG 0.010 0.001 ARG n 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1344 time to evaluate : 6.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 29 ARG cc_start: 0.9450 (mtt180) cc_final: 0.8747 (mtm-85) REVERT: 0 30 THR cc_start: 0.9476 (p) cc_final: 0.9175 (p) REVERT: 0 55 GLN cc_start: 0.8741 (tt0) cc_final: 0.8515 (tt0) REVERT: 0 74 ARG cc_start: 0.8851 (ttp-110) cc_final: 0.8603 (ttp-110) REVERT: 0 78 ASN cc_start: 0.9067 (m110) cc_final: 0.8540 (m110) REVERT: 0 79 LEU cc_start: 0.9202 (mt) cc_final: 0.9000 (mt) REVERT: 1 34 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7597 (ttt-90) REVERT: C 84 ASP cc_start: 0.8736 (t0) cc_final: 0.8365 (t0) REVERT: C 87 ARG cc_start: 0.8188 (mpt180) cc_final: 0.7602 (mpt180) REVERT: C 225 MET cc_start: 0.9204 (mtt) cc_final: 0.8883 (mtt) REVERT: D 2 ILE cc_start: 0.8987 (pt) cc_final: 0.8682 (pt) REVERT: D 18 ASP cc_start: 0.8292 (p0) cc_final: 0.8090 (p0) REVERT: D 42 ASN cc_start: 0.8995 (t0) cc_final: 0.8669 (t0) REVERT: D 96 ILE cc_start: 0.9289 (mt) cc_final: 0.9070 (mt) REVERT: D 128 ARG cc_start: 0.8487 (ptp90) cc_final: 0.8238 (mtp180) REVERT: E 136 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8036 (tp-100) REVERT: F 98 GLU cc_start: 0.8583 (mp0) cc_final: 0.7375 (mp0) REVERT: G 30 ASN cc_start: 0.9038 (t0) cc_final: 0.8661 (t0) REVERT: G 32 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7785 (tm-30) REVERT: G 60 ASP cc_start: 0.8904 (p0) cc_final: 0.8580 (p0) REVERT: G 101 ASN cc_start: 0.8690 (p0) cc_final: 0.8396 (p0) REVERT: G 116 GLN cc_start: 0.9057 (tp40) cc_final: 0.8842 (tp-100) REVERT: G 131 ILE cc_start: 0.9580 (mt) cc_final: 0.8869 (mt) REVERT: G 163 ARG cc_start: 0.9207 (ptp-170) cc_final: 0.8947 (ptp-170) REVERT: H 17 ASP cc_start: 0.8662 (m-30) cc_final: 0.8260 (m-30) REVERT: I 117 MET cc_start: 0.4307 (tpt) cc_final: 0.3333 (tpp) REVERT: J 108 MET cc_start: 0.9065 (mtt) cc_final: 0.8728 (mtt) REVERT: J 128 ASN cc_start: 0.9229 (t0) cc_final: 0.8952 (t0) REVERT: K 106 GLU cc_start: 0.8112 (mp0) cc_final: 0.7717 (mp0) REVERT: L 93 ASN cc_start: 0.8660 (p0) cc_final: 0.8427 (p0) REVERT: M 47 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7431 (tm-30) REVERT: O 3 LYS cc_start: 0.9314 (tppp) cc_final: 0.9001 (ttmm) REVERT: O 76 LYS cc_start: 0.9570 (ttpt) cc_final: 0.9339 (tttm) REVERT: O 89 ASP cc_start: 0.8386 (p0) cc_final: 0.8091 (p0) REVERT: O 112 GLU cc_start: 0.8302 (pp20) cc_final: 0.7849 (pp20) REVERT: P 7 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8185 (tm-30) REVERT: Q 48 ARG cc_start: 0.8941 (tmm-80) cc_final: 0.8663 (ttp80) REVERT: Q 66 ASN cc_start: 0.9184 (t0) cc_final: 0.8883 (t0) REVERT: Q 97 ASP cc_start: 0.8612 (t70) cc_final: 0.8191 (t0) REVERT: R 19 THR cc_start: 0.9202 (m) cc_final: 0.8995 (t) REVERT: R 85 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8748 (ttpp) REVERT: S 52 GLU cc_start: 0.7790 (pt0) cc_final: 0.7588 (pt0) REVERT: T 49 ASN cc_start: 0.8846 (t0) cc_final: 0.8605 (t0) REVERT: U 7 ARG cc_start: 0.7923 (tmt-80) cc_final: 0.7457 (tpt170) REVERT: V 51 GLN cc_start: 0.8927 (pp30) cc_final: 0.8608 (pp30) REVERT: V 55 GLU cc_start: 0.8459 (pm20) cc_final: 0.8216 (pm20) REVERT: W 68 LYS cc_start: 0.9046 (tptp) cc_final: 0.8688 (tptp) REVERT: Y 4 LYS cc_start: 0.8827 (tptp) cc_final: 0.8594 (tptp) REVERT: Y 45 GLN cc_start: 0.8752 (pt0) cc_final: 0.8204 (pt0) REVERT: Z 37 ASP cc_start: 0.8519 (p0) cc_final: 0.8192 (p0) REVERT: Z 52 GLU cc_start: 0.8154 (mp0) cc_final: 0.7829 (mp0) REVERT: Z 74 ILE cc_start: 0.9137 (mm) cc_final: 0.8868 (tp) REVERT: a 36 GLU cc_start: 0.8023 (pt0) cc_final: 0.7228 (pt0) REVERT: e 4 ARG cc_start: 0.8391 (mmt-90) cc_final: 0.7716 (mmt-90) REVERT: g 1038 MET cc_start: 0.7588 (tmm) cc_final: 0.7248 (tmm) REVERT: g 1131 GLN cc_start: 0.6233 (mt0) cc_final: 0.5865 (mt0) REVERT: g 1150 LYS cc_start: 0.8625 (mttt) cc_final: 0.8245 (mttt) REVERT: j 8 ASN cc_start: 0.8974 (t0) cc_final: 0.8588 (t0) REVERT: j 34 ASP cc_start: 0.8665 (t70) cc_final: 0.8356 (t0) REVERT: j 183 ASP cc_start: 0.8949 (t70) cc_final: 0.8698 (t70) REVERT: j 184 TYR cc_start: 0.9375 (t80) cc_final: 0.9149 (t80) REVERT: j 185 ASN cc_start: 0.9336 (t0) cc_final: 0.8581 (t0) REVERT: k 20 PHE cc_start: 0.8428 (m-80) cc_final: 0.8188 (m-80) REVERT: k 70 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.7277 (ttp-170) REVERT: k 74 ASN cc_start: 0.9307 (m-40) cc_final: 0.9106 (m-40) REVERT: k 85 ASN cc_start: 0.8995 (t0) cc_final: 0.8555 (t0) REVERT: l 13 GLU cc_start: 0.8280 (pt0) cc_final: 0.8040 (mt-10) REVERT: l 54 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8213 (mmm-85) REVERT: l 64 MET cc_start: 0.8846 (mmt) cc_final: 0.8631 (mmm) REVERT: l 77 ASN cc_start: 0.9093 (t0) cc_final: 0.8508 (t0) REVERT: l 93 ARG cc_start: 0.8763 (mpp-170) cc_final: 0.8545 (mpp80) REVERT: l 101 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7850 (tp30) REVERT: l 132 ASN cc_start: 0.8864 (t0) cc_final: 0.8554 (t0) REVERT: l 146 ASN cc_start: 0.8878 (p0) cc_final: 0.8225 (m-40) REVERT: m 14 GLN cc_start: 0.8765 (mt0) cc_final: 0.8527 (mt0) REVERT: m 56 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7984 (tttp) REVERT: m 81 ASN cc_start: 0.9215 (t0) cc_final: 0.9003 (t0) REVERT: n 31 MET cc_start: 0.9285 (ttp) cc_final: 0.9069 (ttm) REVERT: n 106 GLU cc_start: 0.8476 (pp20) cc_final: 0.8169 (pp20) REVERT: o 114 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7842 (ttt180) REVERT: p 27 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8359 (pttm) REVERT: p 38 TYR cc_start: 0.9118 (t80) cc_final: 0.8789 (t80) REVERT: p 54 LEU cc_start: 0.8478 (mp) cc_final: 0.7642 (mt) REVERT: p 73 SER cc_start: 0.9306 (m) cc_final: 0.8923 (p) REVERT: p 107 ASP cc_start: 0.8388 (t0) cc_final: 0.8061 (t0) REVERT: q 8 ILE cc_start: 0.9187 (mt) cc_final: 0.8794 (mm) REVERT: q 18 ILE cc_start: 0.9369 (tt) cc_final: 0.9081 (tt) REVERT: r 36 ASP cc_start: 0.8629 (p0) cc_final: 0.8420 (p0) REVERT: r 38 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8757 (mp10) REVERT: r 69 ARG cc_start: 0.7822 (mtp-110) cc_final: 0.7477 (mtp180) REVERT: r 94 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7660 (tm-30) REVERT: s 117 TYR cc_start: 0.7915 (m-80) cc_final: 0.7703 (m-80) REVERT: t 81 MET cc_start: 0.8908 (mtp) cc_final: 0.8640 (mtm) REVERT: u 74 LEU cc_start: 0.9361 (mt) cc_final: 0.9094 (mt) REVERT: u 77 PHE cc_start: 0.9473 (m-80) cc_final: 0.9031 (m-80) REVERT: w 40 ASN cc_start: 0.8530 (t0) cc_final: 0.8295 (t0) REVERT: w 63 GLN cc_start: 0.8650 (mm110) cc_final: 0.8383 (mm-40) REVERT: x 9 GLN cc_start: 0.8697 (tt0) cc_final: 0.8156 (tt0) REVERT: x 19 LYS cc_start: 0.9336 (mtpt) cc_final: 0.8810 (tttp) REVERT: x 27 ARG cc_start: 0.8195 (ptt90) cc_final: 0.7946 (ptt-90) REVERT: y 25 ASP cc_start: 0.8603 (t0) cc_final: 0.8025 (t0) REVERT: z 41 PHE cc_start: 0.8919 (m-10) cc_final: 0.8578 (m-10) REVERT: z 44 MET cc_start: 0.8421 (ptp) cc_final: 0.7973 (ptp) outliers start: 19 outliers final: 6 residues processed: 1357 average time/residue: 1.4059 time to fit residues: 3255.1227 Evaluate side-chains 1174 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1168 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain w residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 883 optimal weight: 10.0000 chunk 792 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 534 optimal weight: 2.9990 chunk 423 optimal weight: 0.5980 chunk 819 optimal weight: 10.0000 chunk 317 optimal weight: 20.0000 chunk 498 optimal weight: 6.9990 chunk 610 optimal weight: 0.6980 chunk 949 optimal weight: 9.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 HIS 6 61 ASN C 134 ASN C 260 ASN D 49 GLN E 9 GLN E 41 GLN F 5 HIS G 143 GLN I 6 GLN I 19 ASN I 34 ASN I 43 ASN J 40 HIS J 58 ASN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 116 GLN Q 20 GLN Q 37 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN X 34 HIS Y 25 GLN Y 27 ASN Z 59 ASN Z 70 HIS a 42 HIS c 13 ASN ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1096 GLN g1131 GLN i 177 ASN j 123 GLN ** k 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN k 152 GLN m 63 ASN n 28 ASN o 18 GLN p 75 GLN q 56 HIS q 64 GLN s 20 ASN s 75 GLN u 4 GLN u 35 ASN w 63 GLN x 31 HIS y 52 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 161729 Z= 0.274 Angle : 0.611 14.944 241893 Z= 0.317 Chirality : 0.037 0.301 30928 Planarity : 0.005 0.116 12967 Dihedral : 23.019 179.653 80895 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.40 % Favored : 90.28 % Rotamer: Outliers : 2.98 % Allowed : 16.54 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.26 % 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: -4.21 (0.09), residues: 5864 helix: -3.11 (0.09), residues: 1695 sheet: -2.38 (0.14), residues: 1137 loop : -2.77 (0.10), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 213 HIS 0.013 0.001 HIS t 12 PHE 0.022 0.001 PHE k 107 TYR 0.021 0.002 TYR F 143 ARG 0.007 0.001 ARG W 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1241 time to evaluate : 6.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 29 ARG cc_start: 0.9537 (mtt180) cc_final: 0.9082 (mtt-85) REVERT: 0 30 THR cc_start: 0.9463 (p) cc_final: 0.9212 (p) REVERT: 0 33 LYS cc_start: 0.9252 (mmtt) cc_final: 0.9045 (mmtt) REVERT: 0 55 GLN cc_start: 0.8750 (tt0) cc_final: 0.8457 (tt0) REVERT: 0 74 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8448 (ttp-170) REVERT: 0 78 ASN cc_start: 0.8931 (m110) cc_final: 0.8316 (m110) REVERT: C 84 ASP cc_start: 0.8741 (t0) cc_final: 0.8247 (t0) REVERT: C 87 ARG cc_start: 0.8143 (mpt180) cc_final: 0.7493 (mpt180) REVERT: D 2 ILE cc_start: 0.9027 (pt) cc_final: 0.8825 (pt) REVERT: D 42 ASN cc_start: 0.9115 (t0) cc_final: 0.8809 (t0) REVERT: E 1 MET cc_start: 0.8277 (tpp) cc_final: 0.7854 (ttm) REVERT: E 136 GLN cc_start: 0.8500 (tp-100) cc_final: 0.7732 (tp-100) REVERT: F 135 GLN cc_start: 0.9244 (pm20) cc_final: 0.7704 (pm20) REVERT: F 177 PHE cc_start: 0.6888 (t80) cc_final: 0.6681 (t80) REVERT: G 30 ASN cc_start: 0.9065 (t0) cc_final: 0.8693 (t0) REVERT: G 32 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7922 (tm-30) REVERT: G 77 ILE cc_start: 0.9413 (mm) cc_final: 0.9184 (mt) REVERT: G 101 ASN cc_start: 0.8750 (p0) cc_final: 0.8210 (p0) REVERT: G 116 GLN cc_start: 0.8998 (tp40) cc_final: 0.8531 (tp-100) REVERT: G 163 ARG cc_start: 0.9158 (ptp-170) cc_final: 0.8890 (ptp-170) REVERT: I 117 MET cc_start: 0.3777 (tpt) cc_final: 0.3418 (tpp) REVERT: J 102 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8294 (mt-10) REVERT: J 108 MET cc_start: 0.8992 (mtt) cc_final: 0.8766 (mtt) REVERT: J 128 ASN cc_start: 0.9163 (t0) cc_final: 0.8911 (t0) REVERT: M 47 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6853 (tm-30) REVERT: M 58 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8522 (mtmm) REVERT: M 60 GLN cc_start: 0.8474 (pp30) cc_final: 0.8150 (pp30) REVERT: O 3 LYS cc_start: 0.9349 (tppp) cc_final: 0.9048 (ttmm) REVERT: O 20 GLU cc_start: 0.8398 (pp20) cc_final: 0.7824 (pp20) REVERT: O 89 ASP cc_start: 0.8309 (p0) cc_final: 0.8019 (p0) REVERT: P 7 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8035 (tm-30) REVERT: Q 97 ASP cc_start: 0.8427 (t70) cc_final: 0.8096 (t0) REVERT: R 2 TYR cc_start: 0.8855 (p90) cc_final: 0.8646 (p90) REVERT: T 4 THR cc_start: 0.9052 (m) cc_final: 0.8742 (t) REVERT: U 7 ARG cc_start: 0.7946 (tmt-80) cc_final: 0.7643 (tpt170) REVERT: U 18 ASP cc_start: 0.9065 (m-30) cc_final: 0.8354 (m-30) REVERT: V 89 ILE cc_start: 0.9623 (mt) cc_final: 0.9410 (mt) REVERT: W 38 VAL cc_start: 0.9374 (t) cc_final: 0.9156 (p) REVERT: W 68 LYS cc_start: 0.8958 (tptp) cc_final: 0.8655 (tptp) REVERT: X 17 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7847 (m110) REVERT: X 43 GLU cc_start: 0.7503 (tt0) cc_final: 0.7230 (tt0) REVERT: X 65 ASP cc_start: 0.7973 (p0) cc_final: 0.7662 (p0) REVERT: Y 45 GLN cc_start: 0.8346 (pt0) cc_final: 0.7951 (pt0) REVERT: Z 37 ASP cc_start: 0.8469 (p0) cc_final: 0.8017 (p0) REVERT: Z 52 GLU cc_start: 0.8205 (mp0) cc_final: 0.7968 (mp0) REVERT: g 1038 MET cc_start: 0.7662 (tmm) cc_final: 0.7121 (tmm) REVERT: j 8 ASN cc_start: 0.9011 (t0) cc_final: 0.8636 (t0) REVERT: j 114 LYS cc_start: 0.8980 (tptt) cc_final: 0.8253 (tppp) REVERT: j 183 ASP cc_start: 0.9134 (t70) cc_final: 0.8605 (t70) REVERT: j 184 TYR cc_start: 0.9278 (t80) cc_final: 0.8941 (t80) REVERT: j 185 ASN cc_start: 0.9117 (t0) cc_final: 0.7777 (t0) REVERT: k 70 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7197 (mmm-85) REVERT: k 74 ASN cc_start: 0.9379 (m-40) cc_final: 0.9168 (m110) REVERT: k 85 ASN cc_start: 0.8980 (t0) cc_final: 0.8476 (t0) REVERT: k 161 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6699 (pp) REVERT: l 54 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8203 (mmm-85) REVERT: l 93 ARG cc_start: 0.8780 (mpp-170) cc_final: 0.8578 (mpp80) REVERT: l 101 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7931 (tp30) REVERT: l 148 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9191 (p0) REVERT: m 35 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8299 (mtmm) REVERT: m 56 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7893 (tttp) REVERT: m 72 ASP cc_start: 0.8901 (p0) cc_final: 0.8058 (p0) REVERT: n 52 GLN cc_start: 0.8490 (mp-120) cc_final: 0.8144 (mp10) REVERT: n 143 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7930 (mtm-85) REVERT: p 27 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8482 (pttt) REVERT: p 37 GLN cc_start: 0.9052 (mt0) cc_final: 0.8783 (mt0) REVERT: p 73 SER cc_start: 0.9216 (m) cc_final: 0.8975 (p) REVERT: p 107 ASP cc_start: 0.8340 (t0) cc_final: 0.8075 (t0) REVERT: q 8 ILE cc_start: 0.9231 (mt) cc_final: 0.8863 (mm) REVERT: r 27 PHE cc_start: 0.9398 (m-80) cc_final: 0.9145 (m-80) REVERT: r 38 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8778 (mp10) REVERT: s 104 CYS cc_start: 0.6936 (t) cc_final: 0.6663 (t) REVERT: s 117 TYR cc_start: 0.7982 (m-80) cc_final: 0.7662 (m-80) REVERT: t 62 LYS cc_start: 0.9145 (mttp) cc_final: 0.8938 (mmtp) REVERT: u 12 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7821 (mptt) REVERT: u 77 PHE cc_start: 0.9530 (m-80) cc_final: 0.9124 (m-80) REVERT: v 68 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8037 (t0) REVERT: x 19 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8890 (tttp) REVERT: y 25 ASP cc_start: 0.8686 (t0) cc_final: 0.8062 (t0) REVERT: y 38 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8865 (mtmt) outliers start: 146 outliers final: 101 residues processed: 1312 average time/residue: 1.4251 time to fit residues: 3264.5219 Evaluate side-chains 1278 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1173 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain T residue 7 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 97 THR Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 35 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 527 optimal weight: 0.2980 chunk 294 optimal weight: 8.9990 chunk 790 optimal weight: 10.0000 chunk 646 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 951 optimal weight: 10.0000 chunk 1027 optimal weight: 20.0000 chunk 847 optimal weight: 3.9990 chunk 943 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 763 optimal weight: 10.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 195 GLN J 47 HIS O 116 GLN Q 20 GLN Q 71 GLN U 74 ASN ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1096 GLN g1131 GLN i 170 HIS j 123 GLN ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN n 28 ASN r 40 ASN s 5 ASN t 52 GLN u 4 GLN ** u 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 37 ASN v 46 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 161729 Z= 0.340 Angle : 0.613 18.113 241893 Z= 0.317 Chirality : 0.038 0.316 30928 Planarity : 0.005 0.118 12967 Dihedral : 22.987 179.112 80895 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.42 % Favored : 89.27 % Rotamer: Outliers : 4.62 % Allowed : 18.44 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.26 % 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: -3.52 (0.10), residues: 5864 helix: -2.06 (0.11), residues: 1683 sheet: -2.16 (0.15), residues: 1147 loop : -2.57 (0.10), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 213 HIS 0.009 0.001 HIS d 31 PHE 0.016 0.002 PHE H 46 TYR 0.025 0.002 TYR h 105 ARG 0.007 0.001 ARG l 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1200 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 GLN cc_start: 0.8722 (mt0) cc_final: 0.8485 (mt0) REVERT: 0 15 GLU cc_start: 0.8048 (pm20) cc_final: 0.7448 (pm20) REVERT: 0 29 ARG cc_start: 0.9504 (mtt180) cc_final: 0.8865 (mtt-85) REVERT: 0 30 THR cc_start: 0.9363 (p) cc_final: 0.9142 (p) REVERT: 0 33 LYS cc_start: 0.9271 (mmtt) cc_final: 0.8997 (mmtt) REVERT: 0 48 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8640 (mm-40) REVERT: 0 74 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8459 (ttp-110) REVERT: 0 78 ASN cc_start: 0.8882 (m110) cc_final: 0.8332 (m110) REVERT: 1 34 ARG cc_start: 0.8089 (ttt-90) cc_final: 0.7876 (tmt170) REVERT: C 84 ASP cc_start: 0.8802 (t0) cc_final: 0.8537 (t0) REVERT: D 42 ASN cc_start: 0.9189 (t0) cc_final: 0.8927 (t0) REVERT: D 181 ASP cc_start: 0.8349 (t0) cc_final: 0.8142 (t0) REVERT: E 136 GLN cc_start: 0.8606 (tp-100) cc_final: 0.7874 (tp-100) REVERT: F 135 GLN cc_start: 0.9203 (pm20) cc_final: 0.7675 (pm20) REVERT: G 30 ASN cc_start: 0.9060 (t0) cc_final: 0.8688 (t0) REVERT: G 32 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7905 (tm-30) REVERT: G 77 ILE cc_start: 0.9393 (mm) cc_final: 0.9184 (mt) REVERT: I 117 MET cc_start: 0.4005 (tpt) cc_final: 0.3556 (tpp) REVERT: J 45 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9065 (p) REVERT: J 108 MET cc_start: 0.8990 (mtt) cc_final: 0.8774 (mtt) REVERT: J 128 ASN cc_start: 0.9142 (t0) cc_final: 0.8905 (t0) REVERT: M 58 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8490 (mtmm) REVERT: M 60 GLN cc_start: 0.8453 (pp30) cc_final: 0.8050 (pp30) REVERT: O 3 LYS cc_start: 0.9345 (tppp) cc_final: 0.9062 (ttmm) REVERT: O 20 GLU cc_start: 0.8434 (pp20) cc_final: 0.8008 (pp20) REVERT: O 89 ASP cc_start: 0.8279 (p0) cc_final: 0.7954 (p0) REVERT: P 7 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Q 97 ASP cc_start: 0.8570 (t70) cc_final: 0.8216 (t0) REVERT: R 37 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7762 (tp30) REVERT: R 53 PHE cc_start: 0.8361 (m-80) cc_final: 0.8078 (m-10) REVERT: S 96 ILE cc_start: 0.9415 (pt) cc_final: 0.9066 (pt) REVERT: U 7 ARG cc_start: 0.7928 (tmt-80) cc_final: 0.7663 (tpt170) REVERT: U 18 ASP cc_start: 0.9037 (m-30) cc_final: 0.8275 (m-30) REVERT: V 89 ILE cc_start: 0.9636 (mt) cc_final: 0.9427 (mt) REVERT: W 68 LYS cc_start: 0.8917 (tptp) cc_final: 0.8399 (tptp) REVERT: X 17 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7937 (m110) REVERT: X 43 GLU cc_start: 0.7597 (tt0) cc_final: 0.7274 (tt0) REVERT: X 65 ASP cc_start: 0.8169 (p0) cc_final: 0.7860 (p0) REVERT: Y 45 GLN cc_start: 0.8356 (pt0) cc_final: 0.7974 (pt0) REVERT: Y 49 ASP cc_start: 0.7831 (m-30) cc_final: 0.7620 (m-30) REVERT: Z 37 ASP cc_start: 0.8528 (p0) cc_final: 0.8080 (p0) REVERT: Z 52 GLU cc_start: 0.8251 (mp0) cc_final: 0.7997 (mp0) REVERT: g 1038 MET cc_start: 0.7554 (tmm) cc_final: 0.7015 (tmm) REVERT: j 8 ASN cc_start: 0.9018 (t0) cc_final: 0.8641 (t0) REVERT: j 114 LYS cc_start: 0.8945 (tptt) cc_final: 0.8597 (tppp) REVERT: j 183 ASP cc_start: 0.9163 (t70) cc_final: 0.8555 (t70) REVERT: j 184 TYR cc_start: 0.9294 (t80) cc_final: 0.8957 (t80) REVERT: j 185 ASN cc_start: 0.9076 (t0) cc_final: 0.8083 (t0) REVERT: k 70 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7264 (mtp180) REVERT: k 74 ASN cc_start: 0.9415 (m-40) cc_final: 0.9185 (m110) REVERT: k 85 ASN cc_start: 0.9143 (t0) cc_final: 0.8594 (t0) REVERT: k 146 ARG cc_start: 0.5327 (mtp85) cc_final: 0.4742 (ttm-80) REVERT: k 161 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6803 (pp) REVERT: l 54 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8242 (mmm-85) REVERT: l 101 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7878 (tp30) REVERT: l 126 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8056 (tptt) REVERT: l 148 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9124 (p0) REVERT: m 17 GLN cc_start: 0.8675 (pm20) cc_final: 0.7579 (pm20) REVERT: m 35 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8293 (mtmm) REVERT: n 28 ASN cc_start: 0.9389 (m-40) cc_final: 0.8961 (m-40) REVERT: n 52 GLN cc_start: 0.8323 (mp-120) cc_final: 0.7997 (mp10) REVERT: n 143 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7991 (mtm-85) REVERT: o 52 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6175 (tm-30) REVERT: p 27 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8631 (pttm) REVERT: p 37 GLN cc_start: 0.9101 (mt0) cc_final: 0.8773 (mt0) REVERT: p 38 TYR cc_start: 0.9143 (t80) cc_final: 0.8761 (t80) REVERT: p 62 ASP cc_start: 0.8817 (t0) cc_final: 0.7926 (m-30) REVERT: p 107 ASP cc_start: 0.8338 (t0) cc_final: 0.8080 (t0) REVERT: q 89 ARG cc_start: 0.8128 (ppt170) cc_final: 0.7732 (ppt170) REVERT: r 27 PHE cc_start: 0.9403 (m-80) cc_final: 0.9186 (m-80) REVERT: r 38 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8672 (mp10) REVERT: s 20 ASN cc_start: 0.8881 (t160) cc_final: 0.8519 (t0) REVERT: s 104 CYS cc_start: 0.7198 (t) cc_final: 0.6919 (t) REVERT: t 12 HIS cc_start: 0.6858 (m90) cc_final: 0.6631 (m90) REVERT: u 12 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7837 (mptt) REVERT: v 68 ASP cc_start: 0.8405 (m-30) cc_final: 0.8094 (t0) REVERT: w 13 LYS cc_start: 0.8158 (mttm) cc_final: 0.7869 (mttp) REVERT: w 63 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7629 (tp-100) REVERT: x 19 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8810 (tttp) REVERT: x 49 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8216 (mm-30) REVERT: x 52 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: y 25 ASP cc_start: 0.8731 (t0) cc_final: 0.8092 (t0) outliers start: 226 outliers final: 172 residues processed: 1336 average time/residue: 1.2963 time to fit residues: 3000.9074 Evaluate side-chains 1331 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1153 time to evaluate : 6.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 118 SER 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 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 LYS Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 7 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 55 GLU Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 126 LYS Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 97 THR Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 5 ASN Chi-restraints excluded: chain s residue 35 THR Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain t residue 8 ASN Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 4 GLN Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain y residue 26 ILE Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 940 optimal weight: 4.9990 chunk 715 optimal weight: 20.0000 chunk 493 optimal weight: 0.0470 chunk 105 optimal weight: 7.9990 chunk 454 optimal weight: 0.2980 chunk 638 optimal weight: 8.9990 chunk 955 optimal weight: 9.9990 chunk 1011 optimal weight: 9.9990 chunk 498 optimal weight: 5.9990 chunk 905 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 overall best weight: 2.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 195 GLN H 11 ASN I 19 ASN I 34 ASN O 116 GLN Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 HIS j 123 GLN k 54 GLN k 136 GLN m 63 ASN p 50 GLN ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 161729 Z= 0.193 Angle : 0.535 15.631 241893 Z= 0.279 Chirality : 0.034 0.291 30928 Planarity : 0.004 0.107 12967 Dihedral : 22.930 179.578 80895 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.95 % Favored : 90.76 % Rotamer: Outliers : 3.94 % Allowed : 20.47 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.25 % 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: -3.10 (0.10), residues: 5864 helix: -1.56 (0.12), residues: 1706 sheet: -1.91 (0.15), residues: 1131 loop : -2.41 (0.10), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 213 HIS 0.006 0.001 HIS d 31 PHE 0.011 0.001 PHE U 96 TYR 0.026 0.001 TYR F 143 ARG 0.009 0.000 ARG 0 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1193 time to evaluate : 6.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 GLN cc_start: 0.8702 (mt0) cc_final: 0.8455 (mt0) REVERT: 0 15 GLU cc_start: 0.7880 (pm20) cc_final: 0.7303 (pm20) REVERT: 0 29 ARG cc_start: 0.9464 (mtt180) cc_final: 0.9071 (mtt-85) REVERT: 0 30 THR cc_start: 0.9348 (p) cc_final: 0.9123 (p) REVERT: 0 33 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8991 (mmtt) REVERT: 0 48 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8778 (mm-40) REVERT: 0 55 GLN cc_start: 0.8706 (tt0) cc_final: 0.8360 (tt0) REVERT: 0 59 ASP cc_start: 0.8630 (m-30) cc_final: 0.8376 (m-30) REVERT: 0 78 ASN cc_start: 0.8836 (m110) cc_final: 0.8281 (m110) REVERT: C 84 ASP cc_start: 0.8787 (t0) cc_final: 0.8336 (t0) REVERT: C 87 ARG cc_start: 0.8044 (mpt180) cc_final: 0.7399 (mpt180) REVERT: D 42 ASN cc_start: 0.9148 (t0) cc_final: 0.8904 (t0) REVERT: E 136 GLN cc_start: 0.8527 (tp-100) cc_final: 0.7912 (tp-100) REVERT: F 127 ASN cc_start: 0.8425 (m-40) cc_final: 0.7767 (m-40) REVERT: F 135 GLN cc_start: 0.9234 (pm20) cc_final: 0.7651 (pm20) REVERT: G 30 ASN cc_start: 0.9040 (t0) cc_final: 0.8686 (t0) REVERT: G 77 ILE cc_start: 0.9336 (mm) cc_final: 0.9123 (mt) REVERT: I 117 MET cc_start: 0.3926 (tpt) cc_final: 0.3393 (tpp) REVERT: J 45 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8972 (p) REVERT: J 108 MET cc_start: 0.8987 (mtt) cc_final: 0.8768 (mtt) REVERT: J 129 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7577 (mm-30) REVERT: L 93 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8393 (p0) REVERT: M 58 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8358 (mtmm) REVERT: M 60 GLN cc_start: 0.8481 (pp30) cc_final: 0.8170 (pp30) REVERT: O 3 LYS cc_start: 0.9338 (tppp) cc_final: 0.9084 (mtpp) REVERT: O 20 GLU cc_start: 0.8434 (pp20) cc_final: 0.8083 (pp20) REVERT: O 61 GLN cc_start: 0.7860 (mp10) cc_final: 0.7660 (mp10) REVERT: P 7 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8140 (tm-30) REVERT: S 52 GLU cc_start: 0.7845 (pt0) cc_final: 0.7637 (pt0) REVERT: S 96 ILE cc_start: 0.9391 (pt) cc_final: 0.9036 (pt) REVERT: U 7 ARG cc_start: 0.7843 (tmt-80) cc_final: 0.7613 (tpt170) REVERT: U 18 ASP cc_start: 0.8912 (m-30) cc_final: 0.8188 (m-30) REVERT: W 83 GLU cc_start: 0.7719 (mp0) cc_final: 0.7290 (mp0) REVERT: X 17 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7821 (m110) REVERT: X 43 GLU cc_start: 0.7675 (tt0) cc_final: 0.7464 (tt0) REVERT: X 65 ASP cc_start: 0.8146 (p0) cc_final: 0.7849 (p0) REVERT: Y 45 GLN cc_start: 0.8318 (pt0) cc_final: 0.7825 (pt0) REVERT: Y 49 ASP cc_start: 0.7923 (m-30) cc_final: 0.7611 (m-30) REVERT: Z 37 ASP cc_start: 0.8533 (p0) cc_final: 0.8146 (p0) REVERT: a 46 ASP cc_start: 0.8465 (p0) cc_final: 0.8147 (p0) REVERT: g 1038 MET cc_start: 0.7533 (tmm) cc_final: 0.7194 (tmm) REVERT: g 1041 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7688 (mp0) REVERT: j 8 ASN cc_start: 0.8988 (t0) cc_final: 0.8721 (t0) REVERT: j 183 ASP cc_start: 0.9108 (t70) cc_final: 0.8591 (t70) REVERT: j 184 TYR cc_start: 0.9186 (t80) cc_final: 0.8931 (t80) REVERT: j 185 ASN cc_start: 0.8983 (t0) cc_final: 0.8531 (t0) REVERT: k 70 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7214 (mtp180) REVERT: k 74 ASN cc_start: 0.9442 (m-40) cc_final: 0.9221 (m110) REVERT: k 146 ARG cc_start: 0.5087 (mtp85) cc_final: 0.4598 (ttm-80) REVERT: k 161 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6800 (pp) REVERT: l 54 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8290 (mmm-85) REVERT: l 101 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7616 (mm-30) REVERT: m 35 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8234 (mtmm) REVERT: n 28 ASN cc_start: 0.9377 (m-40) cc_final: 0.8941 (m-40) REVERT: n 52 GLN cc_start: 0.8266 (mp-120) cc_final: 0.7950 (mp10) REVERT: n 143 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8170 (mtm-85) REVERT: o 58 GLU cc_start: 0.7956 (pm20) cc_final: 0.7641 (pm20) REVERT: p 27 LYS cc_start: 0.8990 (ptmm) cc_final: 0.8451 (pttm) REVERT: p 38 TYR cc_start: 0.9080 (t80) cc_final: 0.8858 (t80) REVERT: p 107 ASP cc_start: 0.8263 (t0) cc_final: 0.8009 (t0) REVERT: q 8 ILE cc_start: 0.9111 (mt) cc_final: 0.8764 (mm) REVERT: q 63 ASP cc_start: 0.8473 (m-30) cc_final: 0.8076 (m-30) REVERT: r 38 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8649 (mp10) REVERT: s 20 ASN cc_start: 0.8895 (t160) cc_final: 0.8559 (t0) REVERT: s 104 CYS cc_start: 0.7328 (t) cc_final: 0.7094 (t) REVERT: t 41 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8173 (mm-30) REVERT: t 78 LYS cc_start: 0.9353 (tptp) cc_final: 0.9139 (tptp) REVERT: u 12 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7832 (mptt) REVERT: u 20 TYR cc_start: 0.8466 (m-10) cc_final: 0.8208 (m-10) REVERT: u 47 LYS cc_start: 0.8378 (mptt) cc_final: 0.8077 (mptt) REVERT: v 68 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8130 (t0) REVERT: w 63 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7618 (tp-100) REVERT: x 19 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8874 (tttp) REVERT: x 52 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: y 25 ASP cc_start: 0.8628 (t0) cc_final: 0.7938 (t0) REVERT: y 35 GLU cc_start: 0.7222 (tm-30) cc_final: 0.7002 (tm-30) outliers start: 193 outliers final: 137 residues processed: 1306 average time/residue: 1.2969 time to fit residues: 2934.6560 Evaluate side-chains 1298 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1155 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 7 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 129 MET Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 155 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ILE Chi-restraints excluded: chain r residue 119 ASN Chi-restraints excluded: chain s residue 35 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 842 optimal weight: 3.9990 chunk 573 optimal weight: 1.9990 chunk 14 optimal weight: 50.0000 chunk 752 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 862 optimal weight: 9.9990 chunk 698 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 907 optimal weight: 0.2980 chunk 255 optimal weight: 50.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 115 GLN E 195 GLN J 128 ASN O 116 GLN Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 HIS j 123 GLN ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 63 ASN p 50 GLN q 58 ASN u 4 GLN w 26 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 161729 Z= 0.257 Angle : 0.555 18.723 241893 Z= 0.288 Chirality : 0.035 0.275 30928 Planarity : 0.004 0.112 12967 Dihedral : 22.903 179.952 80894 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.81 % Favored : 89.90 % Rotamer: Outliers : 5.04 % Allowed : 20.73 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.11), residues: 5864 helix: -1.22 (0.13), residues: 1687 sheet: -1.79 (0.15), residues: 1125 loop : -2.28 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 213 HIS 0.008 0.001 HIS d 31 PHE 0.027 0.001 PHE m 78 TYR 0.025 0.001 TYR F 143 ARG 0.015 0.000 ARG h 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1158 time to evaluate : 6.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7931 (pm20) cc_final: 0.7340 (pm20) REVERT: 0 27 MET cc_start: 0.8571 (ppp) cc_final: 0.8296 (ppp) REVERT: 0 29 ARG cc_start: 0.9419 (mtt180) cc_final: 0.8883 (mtm-85) REVERT: 0 30 THR cc_start: 0.9289 (p) cc_final: 0.9074 (p) REVERT: 0 33 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9053 (mmtt) REVERT: 0 55 GLN cc_start: 0.8701 (tt0) cc_final: 0.8376 (tt0) REVERT: 0 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8370 (m-30) REVERT: 0 78 ASN cc_start: 0.8866 (m110) cc_final: 0.8508 (t0) REVERT: C 84 ASP cc_start: 0.8784 (t0) cc_final: 0.8528 (t0) REVERT: D 42 ASN cc_start: 0.9164 (t0) cc_final: 0.8904 (t0) REVERT: E 136 GLN cc_start: 0.8554 (tp-100) cc_final: 0.7933 (tp-100) REVERT: F 127 ASN cc_start: 0.8481 (m-40) cc_final: 0.7870 (m-40) REVERT: F 135 GLN cc_start: 0.9187 (pm20) cc_final: 0.7598 (pm20) REVERT: G 30 ASN cc_start: 0.9068 (t0) cc_final: 0.8730 (t0) REVERT: G 152 ARG cc_start: 0.8792 (tpt170) cc_final: 0.8351 (tpt170) REVERT: H 11 ASN cc_start: 0.8286 (t0) cc_final: 0.8064 (t0) REVERT: I 117 MET cc_start: 0.4011 (tpt) cc_final: 0.3483 (tpp) REVERT: J 45 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9012 (p) REVERT: J 108 MET cc_start: 0.9023 (mtt) cc_final: 0.8800 (mtt) REVERT: J 129 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7660 (mm-30) REVERT: L 93 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8421 (p0) REVERT: M 58 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8241 (mtmm) REVERT: M 60 GLN cc_start: 0.8464 (pp30) cc_final: 0.8148 (pp30) REVERT: O 3 LYS cc_start: 0.9345 (tppp) cc_final: 0.9072 (ttmm) REVERT: O 20 GLU cc_start: 0.8533 (pp20) cc_final: 0.8231 (pp20) REVERT: O 89 ASP cc_start: 0.8230 (p0) cc_final: 0.7974 (p0) REVERT: P 7 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8174 (tm-30) REVERT: R 37 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7301 (tp30) REVERT: S 52 GLU cc_start: 0.7795 (pt0) cc_final: 0.7553 (pt0) REVERT: S 96 ILE cc_start: 0.9422 (pt) cc_final: 0.9054 (pt) REVERT: U 7 ARG cc_start: 0.7872 (tmt-80) cc_final: 0.7570 (tpt170) REVERT: U 18 ASP cc_start: 0.8973 (m-30) cc_final: 0.8253 (m-30) REVERT: W 68 LYS cc_start: 0.8989 (tptp) cc_final: 0.8638 (tttp) REVERT: W 83 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: X 17 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7900 (m110) REVERT: X 65 ASP cc_start: 0.8176 (p0) cc_final: 0.7873 (p0) REVERT: Y 45 GLN cc_start: 0.8377 (pt0) cc_final: 0.7806 (pt0) REVERT: Y 49 ASP cc_start: 0.7954 (m-30) cc_final: 0.7600 (m-30) REVERT: Z 37 ASP cc_start: 0.8565 (p0) cc_final: 0.8177 (p0) REVERT: a 46 ASP cc_start: 0.8448 (p0) cc_final: 0.8201 (p0) REVERT: g 1038 MET cc_start: 0.7654 (tmm) cc_final: 0.7353 (tmm) REVERT: g 1041 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7773 (mp0) REVERT: g 1080 LYS cc_start: 0.8962 (tptt) cc_final: 0.8616 (tptp) REVERT: j 8 ASN cc_start: 0.9013 (t0) cc_final: 0.8655 (t0) REVERT: j 183 ASP cc_start: 0.8986 (t70) cc_final: 0.8500 (t70) REVERT: j 184 TYR cc_start: 0.9179 (t80) cc_final: 0.8893 (t80) REVERT: j 185 ASN cc_start: 0.9024 (t0) cc_final: 0.8587 (t0) REVERT: k 70 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7394 (mmm-85) REVERT: k 74 ASN cc_start: 0.9426 (m-40) cc_final: 0.9216 (m110) REVERT: k 161 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6802 (pp) REVERT: l 10 GLU cc_start: 0.7104 (pm20) cc_final: 0.6873 (pm20) REVERT: l 54 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8287 (mmm-85) REVERT: l 101 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7691 (mm-30) REVERT: m 1 MET cc_start: 0.7675 (tpp) cc_final: 0.7442 (tpt) REVERT: m 17 GLN cc_start: 0.8361 (pm20) cc_final: 0.7831 (pm20) REVERT: m 35 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8243 (mtmm) REVERT: n 28 ASN cc_start: 0.9355 (m-40) cc_final: 0.8664 (m-40) REVERT: n 52 GLN cc_start: 0.8255 (mp-120) cc_final: 0.7944 (mp10) REVERT: n 143 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8206 (mtm-85) REVERT: p 37 GLN cc_start: 0.9069 (mt0) cc_final: 0.8845 (mt0) REVERT: p 38 TYR cc_start: 0.9092 (t80) cc_final: 0.8871 (t80) REVERT: p 107 ASP cc_start: 0.8295 (t0) cc_final: 0.8051 (t0) REVERT: q 63 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: r 38 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8709 (mp10) REVERT: r 94 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7278 (tm-30) REVERT: s 20 ASN cc_start: 0.8953 (t160) cc_final: 0.8587 (t0) REVERT: s 104 CYS cc_start: 0.7368 (t) cc_final: 0.7159 (t) REVERT: t 78 LYS cc_start: 0.9197 (tptp) cc_final: 0.8919 (tptp) REVERT: u 20 TYR cc_start: 0.8528 (m-10) cc_final: 0.8098 (m-10) REVERT: u 77 PHE cc_start: 0.9556 (m-80) cc_final: 0.9145 (m-80) REVERT: v 68 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8095 (t0) REVERT: w 63 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7781 (tp-100) REVERT: w 67 ILE cc_start: 0.8442 (mm) cc_final: 0.8182 (mm) REVERT: x 49 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8082 (mm-30) REVERT: x 50 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8634 (p0) REVERT: x 52 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: y 25 ASP cc_start: 0.8654 (t0) cc_final: 0.7984 (t0) outliers start: 247 outliers final: 194 residues processed: 1307 average time/residue: 1.2937 time to fit residues: 2935.8626 Evaluate side-chains 1349 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1146 time to evaluate : 6.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 7 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 123 ASP Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 129 MET Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 55 GLU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 36 ASP Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 35 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 26 ILE Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 340 optimal weight: 2.9990 chunk 910 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 593 optimal weight: 6.9990 chunk 249 optimal weight: 50.0000 chunk 1012 optimal weight: 7.9990 chunk 840 optimal weight: 10.0000 chunk 468 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 531 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 115 GLN E 195 GLN I 19 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN Q 20 GLN Q 71 GLN U 74 ASN e 37 GLN ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 59 GLN ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN p 50 GLN q 58 ASN t 14 HIS t 52 GLN u 4 GLN ** u 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 47 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 161729 Z= 0.334 Angle : 0.599 16.852 241893 Z= 0.309 Chirality : 0.037 0.287 30928 Planarity : 0.005 0.115 12967 Dihedral : 22.909 179.161 80894 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.21 % Favored : 89.46 % Rotamer: Outliers : 5.66 % Allowed : 20.87 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.11), residues: 5864 helix: -1.12 (0.13), residues: 1699 sheet: -1.77 (0.15), residues: 1132 loop : -2.26 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 213 HIS 0.009 0.001 HIS d 31 PHE 0.031 0.002 PHE m 78 TYR 0.027 0.002 TYR F 143 ARG 0.007 0.000 ARG x 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1157 time to evaluate : 6.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7982 (pm20) cc_final: 0.7392 (pm20) REVERT: 0 29 ARG cc_start: 0.9431 (mtt180) cc_final: 0.8871 (mtm-85) REVERT: 0 55 GLN cc_start: 0.8692 (tt0) cc_final: 0.8393 (tt0) REVERT: 0 59 ASP cc_start: 0.8622 (m-30) cc_final: 0.8303 (m-30) REVERT: 0 78 ASN cc_start: 0.8878 (m110) cc_final: 0.8522 (t0) REVERT: D 42 ASN cc_start: 0.9186 (t0) cc_final: 0.8919 (t0) REVERT: D 128 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: E 136 GLN cc_start: 0.8551 (tp-100) cc_final: 0.7963 (tp-100) REVERT: F 127 ASN cc_start: 0.8423 (m-40) cc_final: 0.7895 (m-40) REVERT: F 135 GLN cc_start: 0.9181 (pm20) cc_final: 0.7585 (pm20) REVERT: G 30 ASN cc_start: 0.9088 (t0) cc_final: 0.8739 (t0) REVERT: G 152 ARG cc_start: 0.8788 (tpt170) cc_final: 0.8427 (tpt170) REVERT: I 117 MET cc_start: 0.3903 (tpt) cc_final: 0.3243 (tpp) REVERT: J 45 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9051 (p) REVERT: J 108 MET cc_start: 0.8982 (mtt) cc_final: 0.8733 (mtt) REVERT: K 106 GLU cc_start: 0.7776 (mp0) cc_final: 0.7305 (mp0) REVERT: L 93 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8476 (p0) REVERT: M 58 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8250 (mtmm) REVERT: M 60 GLN cc_start: 0.8460 (pp30) cc_final: 0.8115 (pp30) REVERT: O 3 LYS cc_start: 0.9358 (tppp) cc_final: 0.9098 (ttmm) REVERT: O 20 GLU cc_start: 0.8552 (pp20) cc_final: 0.8316 (pp20) REVERT: O 89 ASP cc_start: 0.8306 (p0) cc_final: 0.8059 (p0) REVERT: P 7 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8186 (tm-30) REVERT: R 37 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7347 (tp30) REVERT: S 52 GLU cc_start: 0.7825 (pt0) cc_final: 0.7575 (pt0) REVERT: U 7 ARG cc_start: 0.7974 (tmt-80) cc_final: 0.7699 (tpt170) REVERT: W 68 LYS cc_start: 0.8943 (tptp) cc_final: 0.8547 (tttp) REVERT: W 83 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: X 17 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8021 (m110) REVERT: X 65 ASP cc_start: 0.8187 (p0) cc_final: 0.7875 (p0) REVERT: Y 49 ASP cc_start: 0.7921 (m-30) cc_final: 0.7532 (m-30) REVERT: Z 37 ASP cc_start: 0.8602 (p0) cc_final: 0.8205 (p0) REVERT: Z 52 GLU cc_start: 0.8317 (mp0) cc_final: 0.7963 (mp0) REVERT: a 46 ASP cc_start: 0.8470 (p0) cc_final: 0.8121 (p0) REVERT: g 1038 MET cc_start: 0.7631 (tmm) cc_final: 0.7313 (tmm) REVERT: g 1041 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7772 (mp0) REVERT: h 9 GLN cc_start: 0.0879 (OUTLIER) cc_final: 0.0034 (pp30) REVERT: j 8 ASN cc_start: 0.9035 (t0) cc_final: 0.8691 (t0) REVERT: j 181 ASP cc_start: 0.8568 (t0) cc_final: 0.8335 (t70) REVERT: j 183 ASP cc_start: 0.9045 (t70) cc_final: 0.8412 (t70) REVERT: j 184 TYR cc_start: 0.9214 (t80) cc_final: 0.8943 (t80) REVERT: j 185 ASN cc_start: 0.9075 (t0) cc_final: 0.8738 (t0) REVERT: k 70 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7399 (mmm-85) REVERT: k 74 ASN cc_start: 0.9399 (m-40) cc_final: 0.9197 (m110) REVERT: k 103 TYR cc_start: 0.3946 (t80) cc_final: 0.3682 (t80) REVERT: k 161 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6856 (pp) REVERT: l 54 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8283 (mmm-85) REVERT: l 101 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7810 (mm-30) REVERT: m 1 MET cc_start: 0.7732 (tpp) cc_final: 0.7263 (tpt) REVERT: m 35 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8185 (mtmm) REVERT: m 46 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: n 28 ASN cc_start: 0.9380 (m-40) cc_final: 0.8652 (t0) REVERT: n 52 GLN cc_start: 0.8238 (mp-120) cc_final: 0.7927 (mp10) REVERT: n 129 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: n 143 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8261 (mtm-85) REVERT: p 37 GLN cc_start: 0.9097 (mt0) cc_final: 0.8871 (mt0) REVERT: p 38 TYR cc_start: 0.9097 (t80) cc_final: 0.8890 (t80) REVERT: p 57 MET cc_start: 0.8612 (ppp) cc_final: 0.8100 (ppp) REVERT: p 107 ASP cc_start: 0.8286 (t0) cc_final: 0.8033 (t0) REVERT: p 124 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8673 (mtm110) REVERT: q 63 ASP cc_start: 0.8529 (m-30) cc_final: 0.8214 (m-30) REVERT: r 38 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8722 (mp10) REVERT: r 94 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7459 (tm-30) REVERT: s 20 ASN cc_start: 0.8941 (t160) cc_final: 0.8603 (t0) REVERT: s 70 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: s 104 CYS cc_start: 0.7598 (t) cc_final: 0.7284 (t) REVERT: t 31 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8280 (mtmm) REVERT: t 86 TYR cc_start: 0.8651 (t80) cc_final: 0.8398 (t80) REVERT: u 20 TYR cc_start: 0.8455 (m-10) cc_final: 0.8115 (m-10) REVERT: v 68 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (t0) REVERT: w 63 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7772 (tp-100) REVERT: x 49 GLU cc_start: 0.8861 (mm-30) cc_final: 0.7990 (mm-30) REVERT: x 50 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8805 (p0) REVERT: x 52 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: y 25 ASP cc_start: 0.8609 (t0) cc_final: 0.7918 (t0) REVERT: z 11 ILE cc_start: 0.9054 (mm) cc_final: 0.8791 (mm) outliers start: 277 outliers final: 215 residues processed: 1322 average time/residue: 1.4588 time to fit residues: 3381.6149 Evaluate side-chains 1373 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1146 time to evaluate : 6.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 LYS Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 58 TYR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 123 ASP Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 170 HIS Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 55 GLU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain n residue 129 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 80 THR Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 36 ASP Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ILE Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 5 ASN Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 35 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain s residue 70 GLU Chi-restraints excluded: chain s residue 73 ASN Chi-restraints excluded: chain t residue 8 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 4 GLN Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 22 THR Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 23 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 26 ILE Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 975 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 576 optimal weight: 2.9990 chunk 739 optimal weight: 10.0000 chunk 572 optimal weight: 9.9990 chunk 851 optimal weight: 2.9990 chunk 565 optimal weight: 1.9990 chunk 1008 optimal weight: 9.9990 chunk 630 optimal weight: 0.6980 chunk 614 optimal weight: 0.9990 chunk 465 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN E 195 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Q 71 GLN U 74 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN ** r 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 52 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 161729 Z= 0.154 Angle : 0.521 16.026 241893 Z= 0.271 Chirality : 0.032 0.245 30928 Planarity : 0.004 0.104 12967 Dihedral : 22.911 179.431 80894 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.82 % Favored : 90.91 % Rotamer: Outliers : 3.92 % Allowed : 22.86 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.11), residues: 5864 helix: -0.88 (0.13), residues: 1704 sheet: -1.60 (0.16), residues: 1120 loop : -2.16 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 213 HIS 0.037 0.001 HIS t 14 PHE 0.021 0.001 PHE H 46 TYR 0.024 0.001 TYR F 143 ARG 0.009 0.000 ARG 0 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1177 time to evaluate : 6.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7855 (pm20) cc_final: 0.7322 (pm20) REVERT: 0 55 GLN cc_start: 0.8671 (tt0) cc_final: 0.8297 (tt0) REVERT: 0 59 ASP cc_start: 0.8597 (m-30) cc_final: 0.8349 (m-30) REVERT: 0 78 ASN cc_start: 0.8825 (m110) cc_final: 0.8201 (m110) REVERT: C 84 ASP cc_start: 0.8753 (t0) cc_final: 0.8297 (t0) REVERT: C 87 ARG cc_start: 0.8008 (mpt180) cc_final: 0.7365 (mpt180) REVERT: D 42 ASN cc_start: 0.9109 (t0) cc_final: 0.8873 (t0) REVERT: D 88 GLU cc_start: 0.8323 (mp0) cc_final: 0.8000 (mp0) REVERT: D 183 GLU cc_start: 0.7863 (pm20) cc_final: 0.7581 (pm20) REVERT: E 136 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8262 (tp40) REVERT: F 127 ASN cc_start: 0.8488 (m-40) cc_final: 0.7849 (m-40) REVERT: F 135 GLN cc_start: 0.9240 (pm20) cc_final: 0.7718 (pm20) REVERT: G 30 ASN cc_start: 0.9057 (t0) cc_final: 0.8721 (t0) REVERT: G 152 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8351 (tpt170) REVERT: I 117 MET cc_start: 0.3984 (tpt) cc_final: 0.3449 (tpp) REVERT: J 45 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8913 (p) REVERT: J 108 MET cc_start: 0.8949 (mtt) cc_final: 0.8634 (mtt) REVERT: K 106 GLU cc_start: 0.7730 (mp0) cc_final: 0.7264 (mp0) REVERT: M 58 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8140 (mtmm) REVERT: M 60 GLN cc_start: 0.8407 (pp30) cc_final: 0.8120 (pp30) REVERT: N 20 MET cc_start: 0.8927 (ttp) cc_final: 0.8669 (ttp) REVERT: N 112 TYR cc_start: 0.8877 (m-80) cc_final: 0.8643 (m-80) REVERT: O 3 LYS cc_start: 0.9354 (tppp) cc_final: 0.9087 (ttmm) REVERT: O 20 GLU cc_start: 0.8575 (pp20) cc_final: 0.8305 (pp20) REVERT: P 7 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8181 (tm-30) REVERT: S 52 GLU cc_start: 0.7814 (pt0) cc_final: 0.7580 (pt0) REVERT: U 7 ARG cc_start: 0.7839 (tmt-80) cc_final: 0.7622 (tpt170) REVERT: U 18 ASP cc_start: 0.8903 (m-30) cc_final: 0.8249 (m-30) REVERT: W 68 LYS cc_start: 0.8911 (tptp) cc_final: 0.8558 (tttp) REVERT: W 83 GLU cc_start: 0.7833 (mp0) cc_final: 0.7364 (mp0) REVERT: X 17 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7833 (m110) REVERT: X 65 ASP cc_start: 0.8157 (p0) cc_final: 0.7860 (p0) REVERT: Y 49 ASP cc_start: 0.7856 (m-30) cc_final: 0.7469 (m-30) REVERT: Z 31 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8579 (t) REVERT: Z 37 ASP cc_start: 0.8544 (p0) cc_final: 0.8186 (p0) REVERT: Z 52 GLU cc_start: 0.8321 (mp0) cc_final: 0.7995 (mp0) REVERT: a 46 ASP cc_start: 0.8529 (p0) cc_final: 0.8122 (p0) REVERT: g 1038 MET cc_start: 0.7609 (tmm) cc_final: 0.7335 (tmm) REVERT: g 1041 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7765 (mp0) REVERT: h 9 GLN cc_start: 0.0873 (OUTLIER) cc_final: 0.0030 (pp30) REVERT: j 8 ASN cc_start: 0.8995 (t0) cc_final: 0.8699 (t0) REVERT: j 183 ASP cc_start: 0.9002 (t70) cc_final: 0.8437 (t70) REVERT: j 184 TYR cc_start: 0.9174 (t80) cc_final: 0.8920 (t80) REVERT: j 185 ASN cc_start: 0.8948 (t0) cc_final: 0.8532 (t0) REVERT: j 200 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8836 (m) REVERT: k 21 LEU cc_start: 0.7631 (mt) cc_final: 0.7086 (mt) REVERT: k 70 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7349 (mmm-85) REVERT: k 85 ASN cc_start: 0.9038 (t0) cc_final: 0.8746 (t0) REVERT: k 103 TYR cc_start: 0.3634 (t80) cc_final: 0.3409 (t80) REVERT: k 161 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6978 (pp) REVERT: l 11 LEU cc_start: 0.8608 (mm) cc_final: 0.8406 (mp) REVERT: l 54 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8260 (mmm-85) REVERT: m 1 MET cc_start: 0.7632 (tpp) cc_final: 0.7154 (tpt) REVERT: m 35 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8212 (mtmm) REVERT: n 28 ASN cc_start: 0.9324 (m-40) cc_final: 0.8643 (m-40) REVERT: n 129 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: n 143 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8254 (mtm-85) REVERT: o 60 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6931 (tm-30) REVERT: p 37 GLN cc_start: 0.9125 (mt0) cc_final: 0.8883 (mt0) REVERT: p 38 TYR cc_start: 0.9097 (t80) cc_final: 0.8897 (t80) REVERT: p 57 MET cc_start: 0.8435 (ppp) cc_final: 0.7911 (ppp) REVERT: q 8 ILE cc_start: 0.9072 (mt) cc_final: 0.8724 (mm) REVERT: q 63 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: r 38 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8731 (mp10) REVERT: r 94 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7302 (tm-30) REVERT: s 20 ASN cc_start: 0.8946 (t160) cc_final: 0.8630 (t0) REVERT: s 70 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: u 77 PHE cc_start: 0.9557 (m-80) cc_final: 0.9181 (m-80) REVERT: v 68 ASP cc_start: 0.8425 (m-30) cc_final: 0.8105 (t0) REVERT: w 63 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7789 (tp-100) REVERT: w 67 ILE cc_start: 0.8449 (mm) cc_final: 0.8188 (mm) REVERT: x 49 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7976 (mm-30) REVERT: x 50 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8473 (p0) REVERT: x 52 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: y 25 ASP cc_start: 0.8620 (t0) cc_final: 0.7952 (t0) REVERT: z 20 GLU cc_start: 0.8563 (mp0) cc_final: 0.8342 (mp0) outliers start: 192 outliers final: 152 residues processed: 1293 average time/residue: 1.3050 time to fit residues: 2928.0462 Evaluate side-chains 1309 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1146 time to evaluate : 6.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 GLN Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 30 ILE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 58 TYR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain n residue 129 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 70 GLU Chi-restraints excluded: chain s residue 73 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 34 LEU Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 42 TRP Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 4 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 52 LEU Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 623 optimal weight: 3.9990 chunk 402 optimal weight: 9.9990 chunk 602 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 640 optimal weight: 0.0170 chunk 686 optimal weight: 10.0000 chunk 498 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 792 optimal weight: 10.0000 overall best weight: 4.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN C 251 GLN E 195 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 34 ASN L 54 GLN O 116 GLN Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN g1007 HIS ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN q 58 ASN ** r 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 14 HIS t 52 GLN u 4 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 161729 Z= 0.298 Angle : 0.576 15.760 241893 Z= 0.297 Chirality : 0.035 0.270 30928 Planarity : 0.005 0.113 12967 Dihedral : 22.870 179.799 80894 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.04 % Favored : 89.65 % Rotamer: Outliers : 4.78 % Allowed : 22.59 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.11), residues: 5864 helix: -0.83 (0.13), residues: 1696 sheet: -1.64 (0.15), residues: 1137 loop : -2.13 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 213 HIS 0.008 0.001 HIS d 31 PHE 0.013 0.001 PHE V 26 TYR 0.026 0.002 TYR F 143 ARG 0.011 0.000 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1145 time to evaluate : 6.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7914 (pm20) cc_final: 0.7376 (pm20) REVERT: 0 55 GLN cc_start: 0.8686 (tt0) cc_final: 0.8394 (tt0) REVERT: 0 59 ASP cc_start: 0.8631 (m-30) cc_final: 0.8396 (m-30) REVERT: 0 78 ASN cc_start: 0.8816 (m110) cc_final: 0.8542 (t0) REVERT: D 42 ASN cc_start: 0.9138 (t0) cc_final: 0.8878 (t0) REVERT: E 136 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8041 (tp-100) REVERT: F 127 ASN cc_start: 0.8490 (m-40) cc_final: 0.7836 (m-40) REVERT: F 135 GLN cc_start: 0.9185 (pm20) cc_final: 0.7582 (pm20) REVERT: G 30 ASN cc_start: 0.9096 (t0) cc_final: 0.8751 (t0) REVERT: G 74 SER cc_start: 0.9536 (m) cc_final: 0.8770 (p) REVERT: G 152 ARG cc_start: 0.8740 (tpt170) cc_final: 0.8407 (tpt170) REVERT: I 117 MET cc_start: 0.3716 (tpt) cc_final: 0.3132 (tpp) REVERT: J 45 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9019 (p) REVERT: J 108 MET cc_start: 0.8915 (mtt) cc_final: 0.8559 (mtt) REVERT: K 106 GLU cc_start: 0.7721 (mp0) cc_final: 0.7259 (mp0) REVERT: M 47 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7036 (tm-30) REVERT: M 58 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8160 (mtmm) REVERT: M 60 GLN cc_start: 0.8415 (pp30) cc_final: 0.8088 (pp30) REVERT: O 3 LYS cc_start: 0.9365 (tppp) cc_final: 0.9107 (ttmm) REVERT: P 7 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8219 (tm-30) REVERT: S 52 GLU cc_start: 0.7849 (pt0) cc_final: 0.7604 (pt0) REVERT: T 47 MET cc_start: 0.8986 (mtp) cc_final: 0.8740 (mtt) REVERT: U 7 ARG cc_start: 0.7921 (tmt-80) cc_final: 0.7692 (tpt170) REVERT: W 68 LYS cc_start: 0.8916 (tptp) cc_final: 0.8522 (tttp) REVERT: W 83 GLU cc_start: 0.7870 (mp0) cc_final: 0.7410 (mp0) REVERT: X 17 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7989 (m110) REVERT: X 65 ASP cc_start: 0.8186 (p0) cc_final: 0.7885 (p0) REVERT: Y 49 ASP cc_start: 0.7897 (m-30) cc_final: 0.7515 (m-30) REVERT: Z 37 ASP cc_start: 0.8579 (p0) cc_final: 0.8199 (p0) REVERT: Z 52 GLU cc_start: 0.8346 (mp0) cc_final: 0.7996 (mp0) REVERT: a 46 ASP cc_start: 0.8413 (p0) cc_final: 0.8142 (p0) REVERT: g 1038 MET cc_start: 0.7596 (tmm) cc_final: 0.7340 (tmm) REVERT: g 1041 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7786 (mp0) REVERT: h 9 GLN cc_start: 0.0972 (OUTLIER) cc_final: 0.0109 (pp30) REVERT: j 8 ASN cc_start: 0.9028 (t0) cc_final: 0.8707 (t0) REVERT: j 183 ASP cc_start: 0.9002 (t70) cc_final: 0.8437 (t70) REVERT: j 184 TYR cc_start: 0.9185 (t80) cc_final: 0.8951 (t80) REVERT: j 185 ASN cc_start: 0.9044 (t0) cc_final: 0.8602 (t0) REVERT: k 21 LEU cc_start: 0.7655 (mt) cc_final: 0.7133 (mt) REVERT: k 70 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7638 (mmm-85) REVERT: k 74 ASN cc_start: 0.9273 (m-40) cc_final: 0.8837 (m110) REVERT: k 161 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6853 (pp) REVERT: l 54 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8282 (mmm-85) REVERT: m 1 MET cc_start: 0.7684 (tpp) cc_final: 0.7433 (tpp) REVERT: m 35 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8196 (mtmm) REVERT: m 46 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: n 28 ASN cc_start: 0.9368 (m-40) cc_final: 0.8636 (t0) REVERT: p 38 TYR cc_start: 0.9104 (t80) cc_final: 0.8888 (t80) REVERT: p 57 MET cc_start: 0.8240 (ppp) cc_final: 0.7746 (ppp) REVERT: p 124 ARG cc_start: 0.9001 (ttm-80) cc_final: 0.8695 (mtm110) REVERT: q 8 ILE cc_start: 0.9112 (mt) cc_final: 0.8741 (mm) REVERT: q 63 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: r 38 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8765 (mp10) REVERT: r 94 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7364 (tm-30) REVERT: s 20 ASN cc_start: 0.8949 (t160) cc_final: 0.8623 (t0) REVERT: s 70 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: t 31 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8356 (mtmm) REVERT: u 74 LEU cc_start: 0.9235 (mt) cc_final: 0.8864 (mt) REVERT: u 77 PHE cc_start: 0.9564 (m-80) cc_final: 0.9125 (m-80) REVERT: v 68 ASP cc_start: 0.8446 (m-30) cc_final: 0.8128 (t0) REVERT: w 63 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7790 (tp-100) REVERT: x 49 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8076 (mm-30) REVERT: x 50 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8703 (p0) REVERT: x 52 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: y 25 ASP cc_start: 0.8621 (t0) cc_final: 0.8059 (t0) outliers start: 234 outliers final: 199 residues processed: 1283 average time/residue: 1.3031 time to fit residues: 2907.0653 Evaluate side-chains 1347 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1139 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 GLN Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 31 GLU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 30 ILE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 58 TYR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 123 ILE Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 47 GLU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain s residue 5 ASN Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 70 GLU Chi-restraints excluded: chain s residue 73 ASN Chi-restraints excluded: chain t residue 8 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 42 TRP Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 4 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 52 LEU Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 26 ILE Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 917 optimal weight: 9.9990 chunk 965 optimal weight: 8.9990 chunk 881 optimal weight: 2.9990 chunk 939 optimal weight: 8.9990 chunk 565 optimal weight: 2.9990 chunk 409 optimal weight: 7.9990 chunk 737 optimal weight: 30.0000 chunk 288 optimal weight: 10.0000 chunk 848 optimal weight: 0.9980 chunk 888 optimal weight: 8.9990 chunk 936 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN ** r 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 14 HIS t 52 GLN x 47 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 161729 Z= 0.288 Angle : 0.575 20.174 241893 Z= 0.296 Chirality : 0.035 0.274 30928 Planarity : 0.005 0.112 12967 Dihedral : 22.868 179.813 80894 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.87 % Favored : 89.82 % Rotamer: Outliers : 4.98 % Allowed : 22.77 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.11), residues: 5864 helix: -0.77 (0.13), residues: 1702 sheet: -1.63 (0.16), residues: 1133 loop : -2.12 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 213 HIS 0.008 0.001 HIS d 31 PHE 0.016 0.001 PHE z 41 TYR 0.027 0.002 TYR k 103 ARG 0.013 0.000 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1152 time to evaluate : 6.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7884 (pm20) cc_final: 0.7404 (pm20) REVERT: 0 59 ASP cc_start: 0.8632 (m-30) cc_final: 0.8397 (m-30) REVERT: 0 78 ASN cc_start: 0.8799 (m110) cc_final: 0.8531 (t0) REVERT: D 42 ASN cc_start: 0.9138 (t0) cc_final: 0.8872 (t0) REVERT: D 88 GLU cc_start: 0.8347 (mp0) cc_final: 0.7969 (mp0) REVERT: E 136 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8033 (tp-100) REVERT: F 127 ASN cc_start: 0.8497 (m-40) cc_final: 0.7847 (m-40) REVERT: F 135 GLN cc_start: 0.9183 (pm20) cc_final: 0.7609 (pm20) REVERT: G 30 ASN cc_start: 0.9102 (t0) cc_final: 0.8757 (t0) REVERT: G 74 SER cc_start: 0.9552 (m) cc_final: 0.8846 (p) REVERT: G 152 ARG cc_start: 0.8707 (tpt170) cc_final: 0.8450 (tpt170) REVERT: I 117 MET cc_start: 0.3739 (tpt) cc_final: 0.3159 (tpp) REVERT: J 45 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (p) REVERT: J 108 MET cc_start: 0.8906 (mtt) cc_final: 0.8584 (mtt) REVERT: K 106 GLU cc_start: 0.7730 (mp0) cc_final: 0.7198 (mp0) REVERT: M 47 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7007 (tm-30) REVERT: M 58 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8128 (mtmm) REVERT: M 60 GLN cc_start: 0.8414 (pp30) cc_final: 0.8092 (pp30) REVERT: O 3 LYS cc_start: 0.9366 (tppp) cc_final: 0.9109 (ttmm) REVERT: P 7 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8217 (tm-30) REVERT: S 52 GLU cc_start: 0.7851 (pt0) cc_final: 0.7602 (pt0) REVERT: U 7 ARG cc_start: 0.7873 (tmt-80) cc_final: 0.7645 (tpt170) REVERT: W 68 LYS cc_start: 0.8922 (tptp) cc_final: 0.8521 (tttp) REVERT: W 83 GLU cc_start: 0.7869 (mp0) cc_final: 0.7410 (mp0) REVERT: X 17 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.7977 (m110) REVERT: X 65 ASP cc_start: 0.8186 (p0) cc_final: 0.7882 (p0) REVERT: Y 49 ASP cc_start: 0.7903 (m-30) cc_final: 0.7519 (m-30) REVERT: Z 37 ASP cc_start: 0.8567 (p0) cc_final: 0.8192 (p0) REVERT: Z 52 GLU cc_start: 0.8343 (mp0) cc_final: 0.7990 (mp0) REVERT: a 46 ASP cc_start: 0.8652 (p0) cc_final: 0.8262 (p0) REVERT: g 1038 MET cc_start: 0.7592 (tmm) cc_final: 0.7300 (tmm) REVERT: g 1041 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7791 (mp0) REVERT: h 9 GLN cc_start: 0.0997 (OUTLIER) cc_final: 0.0144 (pp30) REVERT: j 8 ASN cc_start: 0.9042 (t0) cc_final: 0.8699 (t0) REVERT: j 183 ASP cc_start: 0.8990 (t70) cc_final: 0.8436 (t70) REVERT: j 184 TYR cc_start: 0.9174 (t80) cc_final: 0.8947 (t80) REVERT: j 185 ASN cc_start: 0.9040 (t0) cc_final: 0.8577 (t0) REVERT: k 70 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7555 (mmm-85) REVERT: k 74 ASN cc_start: 0.9080 (m-40) cc_final: 0.8752 (m110) REVERT: k 161 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6839 (pp) REVERT: l 54 ARG cc_start: 0.8572 (tpp80) cc_final: 0.8277 (mmm-85) REVERT: m 1 MET cc_start: 0.7663 (tpp) cc_final: 0.7397 (tpp) REVERT: m 35 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8189 (mtmm) REVERT: m 46 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: m 56 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8285 (tttp) REVERT: n 28 ASN cc_start: 0.9341 (m-40) cc_final: 0.8664 (m-40) REVERT: n 129 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: o 60 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6848 (tm-30) REVERT: p 38 TYR cc_start: 0.9098 (t80) cc_final: 0.8875 (t80) REVERT: p 57 MET cc_start: 0.8234 (ppp) cc_final: 0.7738 (ppp) REVERT: p 73 SER cc_start: 0.9180 (m) cc_final: 0.8832 (p) REVERT: p 124 ARG cc_start: 0.9008 (ttm-80) cc_final: 0.8698 (mtm110) REVERT: q 8 ILE cc_start: 0.9150 (mt) cc_final: 0.8793 (mm) REVERT: q 63 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: r 38 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8800 (mp10) REVERT: r 94 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7362 (tm-30) REVERT: s 20 ASN cc_start: 0.8947 (t160) cc_final: 0.8628 (t0) REVERT: s 70 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: u 74 LEU cc_start: 0.9239 (mt) cc_final: 0.8842 (mt) REVERT: u 77 PHE cc_start: 0.9564 (m-80) cc_final: 0.9128 (m-80) REVERT: v 68 ASP cc_start: 0.8446 (m-30) cc_final: 0.8129 (t0) REVERT: w 63 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7792 (tp-100) REVERT: x 49 GLU cc_start: 0.8789 (mm-30) cc_final: 0.7998 (mm-30) REVERT: x 50 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8612 (p0) REVERT: x 52 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: y 25 ASP cc_start: 0.8640 (t0) cc_final: 0.8068 (t0) REVERT: z 20 GLU cc_start: 0.8520 (mp0) cc_final: 0.8306 (mp0) outliers start: 244 outliers final: 215 residues processed: 1303 average time/residue: 1.3058 time to fit residues: 2957.3868 Evaluate side-chains 1359 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1134 time to evaluate : 6.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 35 VAL Chi-restraints excluded: chain 1 residue 31 GLU Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 17 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 30 ILE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain g residue 1130 ILE Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 58 TYR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 123 ILE Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 140 ASN Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 55 GLU Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain n residue 129 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ILE Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain s residue 5 ASN Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 70 GLU Chi-restraints excluded: chain s residue 73 ASN Chi-restraints excluded: chain t residue 8 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 42 TRP Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 4 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 2 VAL Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 52 LEU Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Chi-restraints excluded: chain z residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 616 optimal weight: 8.9990 chunk 993 optimal weight: 6.9990 chunk 606 optimal weight: 1.9990 chunk 471 optimal weight: 2.9990 chunk 690 optimal weight: 20.0000 chunk 1042 optimal weight: 0.9990 chunk 959 optimal weight: 7.9990 chunk 829 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 640 optimal weight: 2.9990 chunk 508 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN m 63 ASN ** r 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 52 GLN u 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 161729 Z= 0.159 Angle : 0.523 20.116 241893 Z= 0.272 Chirality : 0.032 0.256 30928 Planarity : 0.004 0.105 12967 Dihedral : 22.882 179.536 80894 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.87 % Favored : 90.86 % Rotamer: Outliers : 4.02 % Allowed : 23.79 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 5864 helix: -0.61 (0.13), residues: 1708 sheet: -1.48 (0.16), residues: 1118 loop : -2.09 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 201 HIS 0.058 0.001 HIS t 14 PHE 0.015 0.001 PHE 1 37 TYR 0.026 0.001 TYR F 143 ARG 0.013 0.000 ARG G 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11728 Ramachandran restraints generated. 5864 Oldfield, 0 Emsley, 5864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1166 time to evaluate : 6.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 GLU cc_start: 0.7769 (pm20) cc_final: 0.7253 (pm20) REVERT: 0 27 MET cc_start: 0.8433 (ppp) cc_final: 0.8199 (ppp) REVERT: 0 55 GLN cc_start: 0.8655 (tt0) cc_final: 0.8354 (tt0) REVERT: 0 59 ASP cc_start: 0.8628 (m-30) cc_final: 0.8391 (m-30) REVERT: 0 78 ASN cc_start: 0.8823 (m110) cc_final: 0.8289 (m110) REVERT: C 84 ASP cc_start: 0.8763 (t0) cc_final: 0.8520 (t0) REVERT: D 42 ASN cc_start: 0.9099 (t0) cc_final: 0.8838 (t0) REVERT: F 127 ASN cc_start: 0.8483 (m-40) cc_final: 0.7830 (m-40) REVERT: F 135 GLN cc_start: 0.9196 (pm20) cc_final: 0.7724 (pm20) REVERT: G 30 ASN cc_start: 0.9070 (t0) cc_final: 0.8750 (t0) REVERT: G 74 SER cc_start: 0.9534 (m) cc_final: 0.8829 (p) REVERT: G 152 ARG cc_start: 0.8612 (tpt170) cc_final: 0.8332 (tpt170) REVERT: I 117 MET cc_start: 0.3541 (tpt) cc_final: 0.2959 (tpp) REVERT: J 45 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8936 (p) REVERT: J 108 MET cc_start: 0.8859 (mtt) cc_final: 0.8531 (mtt) REVERT: K 106 GLU cc_start: 0.7721 (mp0) cc_final: 0.7040 (mp0) REVERT: M 47 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6925 (tm-30) REVERT: M 58 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8078 (mtmm) REVERT: M 60 GLN cc_start: 0.8422 (pp30) cc_final: 0.8158 (pp30) REVERT: N 20 MET cc_start: 0.8936 (ttp) cc_final: 0.8630 (ttp) REVERT: N 112 TYR cc_start: 0.8900 (m-80) cc_final: 0.8693 (m-80) REVERT: O 3 LYS cc_start: 0.9356 (tppp) cc_final: 0.9098 (ttmm) REVERT: S 52 GLU cc_start: 0.7809 (pt0) cc_final: 0.7567 (pt0) REVERT: U 7 ARG cc_start: 0.7788 (tmt-80) cc_final: 0.7586 (tpt170) REVERT: U 18 ASP cc_start: 0.8882 (m-30) cc_final: 0.8224 (m-30) REVERT: W 68 LYS cc_start: 0.8930 (tptp) cc_final: 0.8558 (tttp) REVERT: W 83 GLU cc_start: 0.7868 (mp0) cc_final: 0.7357 (mp0) REVERT: X 17 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7859 (m110) REVERT: X 65 ASP cc_start: 0.8158 (p0) cc_final: 0.7858 (p0) REVERT: Y 49 ASP cc_start: 0.7854 (m-30) cc_final: 0.7471 (m-30) REVERT: Z 31 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8598 (t) REVERT: Z 37 ASP cc_start: 0.8517 (p0) cc_final: 0.8166 (p0) REVERT: Z 52 GLU cc_start: 0.8332 (mp0) cc_final: 0.7993 (mp0) REVERT: a 46 ASP cc_start: 0.8598 (p0) cc_final: 0.8118 (p0) REVERT: g 1038 MET cc_start: 0.7471 (tmm) cc_final: 0.7226 (tmm) REVERT: g 1041 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7776 (mp0) REVERT: g 1080 LYS cc_start: 0.8929 (tptt) cc_final: 0.8604 (tptp) REVERT: h 9 GLN cc_start: 0.0987 (OUTLIER) cc_final: 0.0135 (pp30) REVERT: j 8 ASN cc_start: 0.9014 (t0) cc_final: 0.8673 (t0) REVERT: j 183 ASP cc_start: 0.8924 (t70) cc_final: 0.8444 (t70) REVERT: j 184 TYR cc_start: 0.9175 (t80) cc_final: 0.8921 (t80) REVERT: j 185 ASN cc_start: 0.8955 (t0) cc_final: 0.8539 (t0) REVERT: j 200 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8829 (m) REVERT: k 70 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7525 (mmm-85) REVERT: k 74 ASN cc_start: 0.9088 (m-40) cc_final: 0.8757 (m110) REVERT: k 161 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7134 (pp) REVERT: l 54 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8259 (mmm-85) REVERT: m 1 MET cc_start: 0.7392 (tpp) cc_final: 0.7157 (tpp) REVERT: m 35 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8208 (mtmm) REVERT: m 46 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: m 56 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8098 (tttp) REVERT: m 59 TYR cc_start: 0.9172 (m-80) cc_final: 0.8681 (m-80) REVERT: n 28 ASN cc_start: 0.9242 (m-40) cc_final: 0.8555 (m-40) REVERT: n 129 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: o 60 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6923 (tm-30) REVERT: p 38 TYR cc_start: 0.9075 (t80) cc_final: 0.8847 (t80) REVERT: p 57 MET cc_start: 0.8323 (ppp) cc_final: 0.7880 (ppp) REVERT: q 8 ILE cc_start: 0.9124 (mt) cc_final: 0.8773 (mm) REVERT: q 63 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: r 38 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8734 (mp10) REVERT: r 94 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7331 (tm-30) REVERT: s 20 ASN cc_start: 0.8938 (t160) cc_final: 0.8647 (t0) REVERT: s 70 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: t 16 VAL cc_start: 0.8412 (t) cc_final: 0.8197 (m) REVERT: u 77 PHE cc_start: 0.9556 (m-80) cc_final: 0.9162 (m-80) REVERT: u 86 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7957 (tm-30) REVERT: v 68 ASP cc_start: 0.8433 (m-30) cc_final: 0.8113 (t0) REVERT: w 63 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7803 (tp-100) REVERT: x 49 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8101 (mm-30) REVERT: x 50 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8518 (p0) REVERT: x 52 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: y 25 ASP cc_start: 0.8740 (t0) cc_final: 0.8425 (t0) REVERT: z 20 GLU cc_start: 0.8560 (mp0) cc_final: 0.8328 (mp0) outliers start: 197 outliers final: 174 residues processed: 1287 average time/residue: 1.4245 time to fit residues: 3222.9766 Evaluate side-chains 1335 residues out of total 4898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1149 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 1 residue 37 PHE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 118 SER 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 17 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 7 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain g residue 1023 VAL Chi-restraints excluded: chain g residue 1130 ILE Chi-restraints excluded: chain h residue 9 GLN Chi-restraints excluded: chain h residue 19 ILE Chi-restraints excluded: chain h residue 58 TYR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 199 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 186 THR Chi-restraints excluded: chain j residue 200 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 123 ILE Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 140 ASN Chi-restraints excluded: chain k residue 161 LEU Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain l residue 90 THR Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 30 THR Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain n residue 129 GLU Chi-restraints excluded: chain n residue 133 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 55 THR Chi-restraints excluded: chain o residue 104 VAL Chi-restraints excluded: chain p residue 30 ILE Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ILE Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 64 THR Chi-restraints excluded: chain s residue 67 ILE Chi-restraints excluded: chain s residue 70 GLU Chi-restraints excluded: chain s residue 73 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 31 ILE Chi-restraints excluded: chain u residue 42 TRP Chi-restraints excluded: chain u residue 46 LEU Chi-restraints excluded: chain v residue 4 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 52 LEU Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 22 VAL Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 50 ASN Chi-restraints excluded: chain x residue 52 GLU Chi-restraints excluded: chain x residue 75 LEU Chi-restraints excluded: chain x residue 78 VAL Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 71 THR Chi-restraints excluded: chain z residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 659 optimal weight: 30.0000 chunk 883 optimal weight: 0.3980 chunk 254 optimal weight: 50.0000 chunk 765 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 831 optimal weight: 40.0000 chunk 347 optimal weight: 2.9990 chunk 853 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 overall best weight: 6.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN E 195 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS Q 20 GLN Q 71 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 HIS ** g1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 GLN ** m 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 14 HIS t 52 GLN u 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.102791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067093 restraints weight = 318549.216| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.18 r_work: 0.2723 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 161729 Z= 0.410 Angle : 0.645 20.172 241893 Z= 0.330 Chirality : 0.039 0.295 30928 Planarity : 0.005 0.116 12967 Dihedral : 22.882 178.899 80894 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.83 % Favored : 88.85 % Rotamer: Outliers : 4.76 % Allowed : 23.16 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.11), residues: 5864 helix: -0.69 (0.13), residues: 1691 sheet: -1.61 (0.16), residues: 1144 loop : -2.10 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 213 HIS 0.011 0.001 HIS d 31 PHE 0.015 0.002 PHE V 26 TYR 0.028 0.002 TYR F 143 ARG 0.012 0.001 ARG G 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43609.08 seconds wall clock time: 759 minutes 49.29 seconds (45589.29 seconds total)