Starting phenix.real_space_refine on Sun Apr 14 15:24:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbt_18320/04_2024/8qbt_18320_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 8 Type Number sf(0) Gaussians K 127 8.98 5 Zn 1 6.06 5 P 4736 5.49 5 Mg 248 5.21 5 S 128 5.16 5 C 69055 2.51 5 N 25961 2.21 5 O 40876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "C GLU 236": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 69": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" 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 ARG 81": "NH1" <-> "NH2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 49": "OE1" <-> "OE2" 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 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "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 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" 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 73": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 79": "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 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 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 8": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "j PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 35": "NH1" <-> "NH2" Residue "j PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 82": "OD1" <-> "OD2" Residue "j ASP 127": "OD1" <-> "OD2" Residue "m PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 54": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 73": "OE1" <-> "OE2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 91": "NH1" <-> "NH2" Residue "o ASP 15": "OD1" <-> "OD2" Residue "o GLU 58": "OE1" <-> "OE2" Residue "p PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 59": "OE1" <-> "OE2" Residue "q ASP 62": "OD1" <-> "OD2" Residue "q ASP 91": "OD1" <-> "OD2" Residue "q ARG 124": "NH1" <-> "NH2" Residue "s PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 83": "OE1" <-> "OE2" Residue "t ARG 56": "NH1" <-> "NH2" Residue "t TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 54": "OD1" <-> "OD2" Residue "v ASP 18": "OD1" <-> "OD2" Residue "y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 20": "OE1" <-> "OE2" Residue "2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 35": "NH1" <-> "NH2" Residue "3 GLU 36": "OE1" <-> "OE2" Residue "3 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "f ARG 131": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141132 Number of models: 1 Model: "" Number of chains: 81 Chain: "A" Number of atoms: 60998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2841, 60998 Classifications: {'RNA': 2841} Modifications used: {'rna2p': 2, 'rna2p_pur': 279, 'rna2p_pyr': 147, 'rna3p': 1, 'rna3p_pur': 1360, 'rna3p_pyr': 1052} Link IDs: {'rna2p': 428, 'rna3p': 2412} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} 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: {'PCIS': 1, 'PTRANS': 5, '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: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1285 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain breaks: 1 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: "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: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "Q" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 941 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} 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: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 435 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 395 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} 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: "i" 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': 90, 'rna3p_pur': 755, 'rna3p_pyr': 575} Link IDs: {'rna2p': 209, 'rna3p': 1329} Chain: "j" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1679 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "m" 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: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "s" 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: "t" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "u" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "v" 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: "w" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 85} 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: "y" 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: "z" 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: "1" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "2" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 1 Chain: "3" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 346 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "4" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "5" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 35, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "6" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1648 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "7" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 66} 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 261 Unusual residues: {' K': 83, ' MG': 178} Classifications: {'undetermined': 261} Link IDs: {None: 260} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Unusual residues: {' K': 37, ' MG': 61} Classifications: {'undetermined': 98} Link IDs: {None: 97} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 1006 Classifications: {'water': 1006} Link IDs: {None: 1005} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 176 Classifications: {'water': 176} Link IDs: {None: 175} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0UA7 SG CYS e 11 116.892 141.654 170.190 1.00 73.02 S ATOM A0UAW SG CYS e 14 115.765 142.690 168.756 1.00 53.79 S ATOM A0UDR SG CYS e 27 118.815 142.563 170.214 1.00 54.27 S Time building chain proxies: 54.54, per 1000 atoms: 0.39 Number of scatterers: 141132 At special positions: 0 Unit cell: (266.5, 272.24, 217.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 127 19.00 S 128 16.00 P 4736 15.00 Mg 248 11.99 O 40876 8.00 N 25961 7.00 C 69055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.52 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN e 100 " pdb="ZN ZN e 100 " - pdb=" ND1 HIS e 33 " pdb="ZN ZN e 100 " - pdb=" SG CYS e 11 " pdb="ZN ZN e 100 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 100 " - pdb=" SG CYS e 14 " Number of angles added : 3 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8876 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 146 helices and 62 sheets defined 37.8% alpha, 19.1% beta 1584 base pairs and 2477 stacking pairs defined. Time for finding SS restraints: 72.49 Creating SS restraints... Processing helix chain 'C' and resid 10 through 17 removed outlier: 7.638A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.786A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.588A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.898A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.960A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 6.201A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.744A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.896A pdb=" N PHE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.640A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.536A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.627A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'F' and resid 2 through 21 removed outlier: 4.562A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.951A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.758A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.736A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.603A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.972A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.646A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 47 removed outlier: 4.081A pdb=" N PHE H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.761A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.203A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.006A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.323A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.658A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.787A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.895A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.766A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.115A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.088A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.436A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.128A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.663A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.811A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.624A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.019A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.483A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.562A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.717A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.516A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.887A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.981A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.720A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.548A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.005A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.552A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 1 through 9 removed outlier: 4.241A pdb=" N GLU Y 5 " --> pdb=" O MET Y 1 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 22 Processing helix chain 'Y' and resid 24 through 35 removed outlier: 3.529A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 63 removed outlier: 4.764A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 9 through 19 removed outlier: 4.760A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 24 removed outlier: 4.214A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 38 Processing helix chain 'd' and resid 7 through 14 removed outlier: 3.633A pdb=" N ARG d 13 " --> pdb=" O GLY d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 37 removed outlier: 4.459A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 32 through 37' Processing helix chain 'd' and resid 38 through 46 Proline residue: d 46 - end of helix Processing helix chain 'd' and resid 51 through 63 removed outlier: 4.508A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'j' and resid 24 through 29 removed outlier: 4.307A pdb=" N LYS j 28 " --> pdb=" O ASN j 24 " (cutoff:3.500A) Proline residue: j 29 - end of helix No H-bonds generated for 'chain 'j' and resid 24 through 29' Processing helix chain 'j' and resid 42 through 64 Proline residue: j 48 - end of helix removed outlier: 3.713A pdb=" N GLU j 56 " --> pdb=" O GLU j 52 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG j 63 " --> pdb=" O LYS j 59 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 86 removed outlier: 4.818A pdb=" N GLU j 78 " --> pdb=" O ARG j 74 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA j 79 " --> pdb=" O ALA j 75 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS j 81 " --> pdb=" O SER j 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU j 85 " --> pdb=" O LYS j 81 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER j 86 " --> pdb=" O ASP j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 123 removed outlier: 4.263A pdb=" N GLN j 109 " --> pdb=" O LYS j 105 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER j 110 " --> pdb=" O THR j 106 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN j 122 " --> pdb=" O GLU j 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP j 123 " --> pdb=" O THR j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 148 removed outlier: 3.662A pdb=" N GLU j 142 " --> pdb=" O THR j 138 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER j 147 " --> pdb=" O LYS j 143 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 165 through 170 Processing helix chain 'j' and resid 171 through 180 Processing helix chain 'j' and resid 206 through 224 removed outlier: 3.534A pdb=" N GLU j 223 " --> pdb=" O ALA j 219 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY j 224 " --> pdb=" O THR j 220 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 71 removed outlier: 3.615A pdb=" N ARG m 69 " --> pdb=" O GLU m 65 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN m 70 " --> pdb=" O LYS m 66 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET m 71 " --> pdb=" O ALA m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 108 through 119 removed outlier: 3.569A pdb=" N ALA m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL m 114 " --> pdb=" O ALA m 110 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 147 removed outlier: 3.568A pdb=" N MET m 147 " --> pdb=" O GLY m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 149 through 158 Processing helix chain 'n' and resid 14 through 33 removed outlier: 3.833A pdb=" N VAL n 18 " --> pdb=" O GLN n 14 " (cutoff:3.500A) Proline residue: n 19 - end of helix removed outlier: 3.635A pdb=" N ALA n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU n 33 " --> pdb=" O ILE n 29 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 81 removed outlier: 3.523A pdb=" N ILE n 71 " --> pdb=" O PRO n 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 31 Processing helix chain 'o' and resid 35 through 55 Processing helix chain 'o' and resid 57 through 70 removed outlier: 3.567A pdb=" N ASN o 68 " --> pdb=" O VAL o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 112 removed outlier: 5.678A pdb=" N GLY o 112 " --> pdb=" O ALA o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 115 through 130 Processing helix chain 'o' and resid 132 through 149 Processing helix chain 'p' and resid 5 through 21 Processing helix chain 'p' and resid 30 through 44 Processing helix chain 'p' and resid 112 through 120 Processing helix chain 'q' and resid 34 through 39 Processing helix chain 'q' and resid 45 through 56 removed outlier: 4.436A pdb=" N ARG q 49 " --> pdb=" O ARG q 45 " (cutoff:3.500A) Proline residue: q 51 - end of helix removed outlier: 3.999A pdb=" N LEU q 54 " --> pdb=" O GLN q 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL q 55 " --> pdb=" O PRO q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 88 removed outlier: 4.530A pdb=" N MET q 88 " --> pdb=" O THR q 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 92 through 102 removed outlier: 4.506A pdb=" N SER q 96 " --> pdb=" O GLU q 92 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLU q 97 " --> pdb=" O SER q 93 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 51 removed outlier: 4.459A pdb=" N GLY s 51 " --> pdb=" O ALA s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 54 through 59 removed outlier: 3.823A pdb=" N SER s 58 " --> pdb=" O GLY s 54 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR s 59 " --> pdb=" O SER s 55 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 54 through 59' Processing helix chain 's' and resid 60 through 76 removed outlier: 4.474A pdb=" N ALA s 73 " --> pdb=" O ARG s 69 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL s 74 " --> pdb=" O CYS s 70 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU s 76 " --> pdb=" O ASP s 72 " (cutoff:3.500A) Processing helix chain 's' and resid 92 through 104 removed outlier: 4.375A pdb=" N THR s 96 " --> pdb=" O GLY s 92 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE s 97 " --> pdb=" O ARG s 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY s 104 " --> pdb=" O LEU s 100 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 11 Proline residue: t 11 - end of helix Processing helix chain 't' and resid 113 through 118 Processing helix chain 'u' and resid 14 through 22 removed outlier: 3.840A pdb=" N THR u 20 " --> pdb=" O VAL u 16 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER u 21 " --> pdb=" O ILE u 17 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE u 22 " --> pdb=" O ALA u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 38 Processing helix chain 'u' and resid 44 through 49 removed outlier: 5.158A pdb=" N SER u 49 " --> pdb=" O ILE u 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 50 through 64 removed outlier: 3.903A pdb=" N LYS u 62 " --> pdb=" O ASP u 58 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE u 63 " --> pdb=" O GLU u 59 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 84 removed outlier: 3.589A pdb=" N LEU u 80 " --> pdb=" O SER u 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 85 through 94 Processing helix chain 'u' and resid 106 through 111 Processing helix chain 'v' and resid 3 through 20 removed outlier: 3.562A pdb=" N GLU v 10 " --> pdb=" O MET v 6 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR v 20 " --> pdb=" O LEU v 16 " (cutoff:3.500A) Processing helix chain 'v' and resid 23 through 33 removed outlier: 3.561A pdb=" N LEU v 27 " --> pdb=" O LYS v 23 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS v 28 " --> pdb=" O ARG v 24 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP v 33 " --> pdb=" O ALA v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 50 removed outlier: 3.847A pdb=" N LYS v 47 " --> pdb=" O ASN v 43 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR v 50 " --> pdb=" O LEU v 46 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 91 removed outlier: 3.611A pdb=" N ARG v 85 " --> pdb=" O ARG v 81 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 16 Processing helix chain 'w' and resid 24 through 43 removed outlier: 3.516A pdb=" N GLN w 40 " --> pdb=" O ILE w 36 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY w 41 " --> pdb=" O ASN w 37 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS w 42 " --> pdb=" O HIS w 38 " (cutoff:3.500A) Processing helix chain 'w' and resid 49 through 74 removed outlier: 3.677A pdb=" N GLY w 55 " --> pdb=" O HIS w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 86 Processing helix chain 'z' and resid 25 through 34 removed outlier: 3.886A pdb=" N ASN z 31 " --> pdb=" O ALA z 27 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR z 32 " --> pdb=" O THR z 28 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR z 34 " --> pdb=" O LYS z 30 " (cutoff:3.500A) Processing helix chain 'z' and resid 41 through 46 Processing helix chain 'z' and resid 48 through 66 Processing helix chain '1' and resid 12 through 26 removed outlier: 3.528A pdb=" N GLU 1 24 " --> pdb=" O GLU 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 76 removed outlier: 4.439A pdb=" N PHE 1 74 " --> pdb=" O LYS 1 70 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA 1 75 " --> pdb=" O LEU 1 71 " (cutoff:3.500A) Proline residue: 1 76 - end of helix No H-bonds generated for 'chain '1' and resid 70 through 76' Processing helix chain '2' and resid 6 through 41 removed outlier: 5.265A pdb=" N ARG 2 10 " --> pdb=" O SER 2 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 2 35 " --> pdb=" O PHE 2 31 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 62 Proline residue: 2 56 - end of helix removed outlier: 3.933A pdb=" N ALA 2 62 " --> pdb=" O VAL 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 87 removed outlier: 3.900A pdb=" N LEU 2 86 " --> pdb=" O GLN 2 82 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 24 removed outlier: 4.635A pdb=" N ARG 3 21 " --> pdb=" O ARG 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 25 through 34 removed outlier: 4.723A pdb=" N ARG 3 34 " --> pdb=" O ALA 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 53 Proline residue: 3 41 - end of helix removed outlier: 3.563A pdb=" N LYS 3 49 " --> pdb=" O ARG 3 45 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL 3 53 " --> pdb=" O LYS 3 49 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.490A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.502A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.008A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.079A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.643A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.497A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.350A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.335A pdb=" N LEU E 5 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.754A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 65 through 68 removed outlier: 5.822A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.640A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 41 through 44 Processing sheet with id= 13, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 14, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.623A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 2 through 5 removed outlier: 4.376A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.883A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.498A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.325A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 20, first strand: chain 'L' and resid 120 through 123 Processing sheet with id= 21, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.559A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.769A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.957A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'O' and resid 49 through 53 removed outlier: 6.644A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.572A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.768A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.604A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.221A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 31, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 32, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.217A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 34, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.290A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 40 through 45 removed outlier: 4.675A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 82 through 86 removed outlier: 7.208A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU U 101 " --> pdb=" O PHE U 96 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.497A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.011A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 40, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.505A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 42, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.403A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.328A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 19 through 26 removed outlier: 6.049A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.524A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 90 through 93 removed outlier: 3.611A pdb=" N ILE j 186 " --> pdb=" O VAL j 163 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 12 through 16 removed outlier: 6.735A pdb=" N LEU m 36 " --> pdb=" O ILE m 16 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 84 through 88 removed outlier: 3.696A pdb=" N ALA m 99 " --> pdb=" O ASN m 122 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN m 122 " --> pdb=" O ALA m 99 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'm' and resid 33 through 40 Processing sheet with id= 50, first strand: chain 'n' and resid 38 through 42 removed outlier: 5.846A pdb=" N TYR n 59 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS n 3 " --> pdb=" O THR n 92 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'n' and resid 43 through 47 removed outlier: 6.067A pdb=" N LEU n 47 " --> pdb=" O HIS n 55 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HIS n 55 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 72 through 79 removed outlier: 6.245A pdb=" N THR o 72 " --> pdb=" O VAL o 91 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL o 87 " --> pdb=" O LYS o 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG o 78 " --> pdb=" O TYR o 85 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR o 85 " --> pdb=" O ARG o 78 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 23 through 29 removed outlier: 6.148A pdb=" N ALA p 23 " --> pdb=" O LEU p 63 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP p 48 " --> pdb=" O THR p 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 74 through 77 removed outlier: 6.752A pdb=" N VAL p 103 " --> pdb=" O ILE p 126 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 5 through 11 removed outlier: 4.433A pdb=" N GLY q 10 " --> pdb=" O ALA q 17 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS q 22 " --> pdb=" O ASP q 62 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS q 27 " --> pdb=" O LEU q 61 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 42 through 45 Processing sheet with id= 57, first strand: chain 't' and resid 29 through 33 removed outlier: 5.041A pdb=" N LEU t 81 " --> pdb=" O VAL t 98 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 36 through 41 removed outlier: 3.697A pdb=" N ARG t 36 " --> pdb=" O ARG t 54 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS t 51 " --> pdb=" O ILE t 67 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'y' and resid 7 through 11 removed outlier: 6.868A pdb=" N GLU y 60 " --> pdb=" O VAL y 76 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'y' and resid 20 through 30 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain '1' and resid 30 through 34 removed outlier: 4.843A pdb=" N LEU 1 47 " --> pdb=" O VAL 1 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 14 through 19 1554 hydrogen bonds defined for protein. 4566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3973 hydrogen bonds 6216 hydrogen bond angles 0 basepair planarities 1584 basepair parallelities 2477 stacking parallelities Total time for adding SS restraints: 402.37 Time building geometry restraints manager: 66.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15112 1.32 - 1.46: 75160 1.46 - 1.59: 52442 1.59 - 1.72: 9264 1.72 - 1.85: 229 Bond restraints: 152207 Sorted by residual: bond pdb=" N3 2MA A2503 " pdb=" C4 2MA A2503 " ideal model delta sigma weight residual 1.488 1.347 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C5 2MA A2503 " pdb=" C6 2MA A2503 " ideal model delta sigma weight residual 1.540 1.407 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C2 2MA A2503 " pdb=" N3 2MA A2503 " ideal model delta sigma weight residual 1.462 1.345 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" O5' C i 110 " pdb=" C5' C i 110 " ideal model delta sigma weight residual 1.420 1.492 -0.072 1.50e-02 4.44e+03 2.28e+01 bond pdb=" CD ARG C 221 " pdb=" NE ARG C 221 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.00e+01 ... (remaining 152202 not shown) Histogram of bond angle deviations from ideal: 76.37 - 88.30: 11 88.30 - 100.23: 4641 100.23 - 112.16: 96919 112.16 - 124.09: 105652 124.09 - 136.02: 21778 Bond angle restraints: 229001 Sorted by residual: angle pdb=" O3' U A2296 " pdb=" P A A2297 " pdb=" O5' A A2297 " ideal model delta sigma weight residual 104.00 76.55 27.45 1.50e+00 4.44e-01 3.35e+02 angle pdb=" O3' A A 685 " pdb=" P U A 686 " pdb=" O5' U A 686 " ideal model delta sigma weight residual 104.00 78.50 25.50 1.50e+00 4.44e-01 2.89e+02 angle pdb=" O3' C A 994 " pdb=" P C A 995 " pdb=" O5' C A 995 " ideal model delta sigma weight residual 104.00 84.77 19.23 1.50e+00 4.44e-01 1.64e+02 angle pdb=" O3' G i 500 " pdb=" P C i 501 " pdb=" O5' C i 501 " ideal model delta sigma weight residual 104.00 85.05 18.95 1.50e+00 4.44e-01 1.60e+02 angle pdb=" O3' C i 501 " pdb=" P A i 502 " pdb=" O5' A i 502 " ideal model delta sigma weight residual 104.00 85.06 18.94 1.50e+00 4.44e-01 1.59e+02 ... (remaining 228996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 86938 35.93 - 71.86: 9788 71.86 - 107.79: 1016 107.79 - 143.72: 21 143.72 - 179.65: 33 Dihedral angle restraints: 97796 sinusoidal: 84027 harmonic: 13769 Sorted by residual: dihedral pdb=" C5' C A2146 " pdb=" C4' C A2146 " pdb=" C3' C A2146 " pdb=" O3' C A2146 " ideal model delta sinusoidal sigma weight residual 147.00 79.20 67.80 1 8.00e+00 1.56e-02 9.33e+01 dihedral pdb=" C4' C A2146 " pdb=" C3' C A2146 " pdb=" C2' C A2146 " pdb=" C1' C A2146 " ideal model delta sinusoidal sigma weight residual -35.00 31.89 -66.89 1 8.00e+00 1.56e-02 9.11e+01 dihedral pdb=" O4' C 5 57 " pdb=" C1' C 5 57 " pdb=" N1 C 5 57 " pdb=" C2 C 5 57 " ideal model delta sinusoidal sigma weight residual 200.00 21.32 178.68 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 97793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 25420 0.165 - 0.330: 3944 0.330 - 0.495: 66 0.495 - 0.660: 12 0.660 - 0.825: 2 Chirality restraints: 29444 Sorted by residual: chirality pdb=" C3' G i 115 " pdb=" C4' G i 115 " pdb=" O3' G i 115 " pdb=" C2' G i 115 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C3* PSU A 746 " pdb=" C4* PSU A 746 " pdb=" O3* PSU A 746 " pdb=" C2* PSU A 746 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3' A i1201 " pdb=" C4' A i1201 " pdb=" O3' A i1201 " pdb=" C2' A i1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 29441 not shown) Planarity restraints: 11367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 512 " 0.163 2.00e-02 2.50e+03 6.33e-02 1.20e+02 pdb=" N9 G A 512 " -0.092 2.00e-02 2.50e+03 pdb=" C8 G A 512 " -0.036 2.00e-02 2.50e+03 pdb=" N7 G A 512 " -0.038 2.00e-02 2.50e+03 pdb=" C5 G A 512 " -0.017 2.00e-02 2.50e+03 pdb=" C6 G A 512 " 0.049 2.00e-02 2.50e+03 pdb=" O6 G A 512 " 0.051 2.00e-02 2.50e+03 pdb=" N1 G A 512 " 0.035 2.00e-02 2.50e+03 pdb=" C2 G A 512 " -0.024 2.00e-02 2.50e+03 pdb=" N2 G A 512 " -0.021 2.00e-02 2.50e+03 pdb=" N3 G A 512 " -0.044 2.00e-02 2.50e+03 pdb=" C4 G A 512 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 258 " -0.787 9.50e-02 1.11e+02 3.55e-01 1.00e+02 pdb=" NE ARG C 258 " 0.078 2.00e-02 2.50e+03 pdb=" CZ ARG C 258 " -0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG C 258 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 258 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 51 " 0.872 9.50e-02 1.11e+02 3.91e-01 9.73e+01 pdb=" NE ARG Q 51 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG Q 51 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 51 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 51 " 0.011 2.00e-02 2.50e+03 ... (remaining 11364 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.05: 579 2.05 - 2.82: 37483 2.82 - 3.60: 263570 3.60 - 4.37: 550787 4.37 - 5.14: 741183 Nonbonded interactions: 1593602 Sorted by model distance: nonbonded pdb=" O3' A 6 76 " pdb=" C PRO f 133 " model vdw 1.281 3.270 nonbonded pdb=" O3' A 5 77 " pdb=" C PRO 5 101 " model vdw 1.298 3.270 nonbonded pdb="MG MG A6035 " pdb=" O HOH A6672 " model vdw 1.800 2.170 nonbonded pdb="MG MG A6074 " pdb=" O HOH A6861 " model vdw 1.843 2.170 nonbonded pdb="MG MG A6139 " pdb=" O HOH A7167 " model vdw 1.845 2.170 ... (remaining 1593597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and resid 1 through 77) selection = (chain '6' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name N4 or name C5 or name C6 )) or resid 2 thr \ ough 76)) } 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: 4.100 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: 15.650 Check model and map are aligned: 1.500 Set scattering table: 0.960 Process input model: 719.010 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 757.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.008 0.141 152207 Z= 0.505 Angle : 1.706 31.631 229001 Z= 1.046 Chirality : 0.111 0.825 29444 Planarity : 0.019 0.391 11367 Dihedral : 22.930 179.650 88920 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.47 % Favored : 94.30 % Rotamer: Outliers : 0.91 % Allowed : 6.93 % Favored : 92.15 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.11 (0.11), residues: 4751 helix: -1.26 (0.11), residues: 1521 sheet: -1.39 (0.15), residues: 923 loop : -1.38 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.007 TRP C 248 HIS 0.026 0.004 HIS a 19 PHE 0.052 0.006 PHE 1 10 TYR 0.052 0.006 TYR Q 32 ARG 0.086 0.004 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1043 time to evaluate : 5.521 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5787 (mttt) cc_final: 0.5254 (tptm) REVERT: C 13 ARG cc_start: 0.7337 (tpt170) cc_final: 0.7035 (mmm160) REVERT: C 25 HIS cc_start: 0.6584 (t-90) cc_final: 0.6246 (t70) REVERT: C 100 GLU cc_start: 0.6387 (tt0) cc_final: 0.6091 (tt0) REVERT: C 111 LYS cc_start: 0.5394 (ptmm) cc_final: 0.4839 (pttp) REVERT: C 114 ASP cc_start: 0.5344 (m-30) cc_final: 0.4764 (m-30) REVERT: C 125 LYS cc_start: 0.5415 (pttt) cc_final: 0.4472 (mmmt) REVERT: C 133 ARG cc_start: 0.5660 (ptt-90) cc_final: 0.4923 (ttm-80) REVERT: C 134 ASN cc_start: 0.6960 (m110) cc_final: 0.6600 (m-40) REVERT: C 146 MET cc_start: 0.7241 (mtp) cc_final: 0.6807 (mtt) REVERT: C 163 GLN cc_start: 0.6870 (tt0) cc_final: 0.6294 (mt0) REVERT: C 175 ARG cc_start: 0.6768 (ttm-80) cc_final: 0.6545 (ttm110) REVERT: C 177 ARG cc_start: 0.6757 (tpt90) cc_final: 0.6500 (mtp180) REVERT: C 183 LYS cc_start: 0.6108 (mttt) cc_final: 0.5848 (mtpp) REVERT: C 185 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6258 (mt-10) REVERT: C 194 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6632 (mt-10) REVERT: C 201 MET cc_start: 0.7006 (ptt) cc_final: 0.6736 (ptm) REVERT: C 203 ARG cc_start: 0.6148 (ptt180) cc_final: 0.5875 (ptp-110) REVERT: C 214 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6797 (mtt90) REVERT: C 265 LYS cc_start: 0.5666 (tttm) cc_final: 0.5328 (ptpt) REVERT: C 269 ARG cc_start: 0.5901 (ttp-170) cc_final: 0.5170 (ttp80) REVERT: D 7 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6646 (tttp) REVERT: D 11 MET cc_start: 0.7650 (mtp) cc_final: 0.7403 (mtp) REVERT: D 17 GLU cc_start: 0.3917 (tt0) cc_final: 0.3632 (mp0) REVERT: D 55 LYS cc_start: 0.5072 (ttmm) cc_final: 0.4836 (mtmt) REVERT: D 70 LYS cc_start: 0.5184 (tttt) cc_final: 0.4695 (tptt) REVERT: D 74 GLU cc_start: 0.5452 (tt0) cc_final: 0.4951 (mp0) REVERT: D 95 SER cc_start: 0.6025 (m) cc_final: 0.5739 (t) REVERT: D 99 GLU cc_start: 0.5374 (tp30) cc_final: 0.4937 (pt0) REVERT: D 101 PHE cc_start: 0.5807 (m-80) cc_final: 0.5385 (m-80) REVERT: D 105 LYS cc_start: 0.5821 (mttt) cc_final: 0.5530 (mmmt) REVERT: D 128 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6622 (mtt180) REVERT: D 131 ASP cc_start: 0.7137 (m-30) cc_final: 0.6805 (m-30) REVERT: D 157 LYS cc_start: 0.6752 (mttt) cc_final: 0.6412 (mmtm) REVERT: D 173 GLN cc_start: 0.6814 (mt0) cc_final: 0.6515 (mt0) REVERT: D 200 ASP cc_start: 0.7205 (m-30) cc_final: 0.6908 (m-30) REVERT: D 204 LYS cc_start: 0.6571 (mtmm) cc_final: 0.6205 (mtpt) REVERT: E 23 PHE cc_start: 0.6278 (t80) cc_final: 0.6018 (t80) REVERT: E 57 LYS cc_start: 0.6523 (tttp) cc_final: 0.6314 (tptm) REVERT: E 61 ARG cc_start: 0.7085 (ptm160) cc_final: 0.6413 (ptt-90) REVERT: E 105 LEU cc_start: 0.6741 (mt) cc_final: 0.6418 (mt) REVERT: E 111 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5805 (tp30) REVERT: E 120 VAL cc_start: 0.5003 (t) cc_final: 0.4645 (p) REVERT: E 130 LYS cc_start: 0.4601 (mmtm) cc_final: 0.3921 (tppt) REVERT: E 132 LYS cc_start: 0.4321 (mtpp) cc_final: 0.3970 (ttmm) REVERT: E 141 MET cc_start: 0.3834 (mtp) cc_final: 0.3482 (ttp) REVERT: E 163 ASN cc_start: 0.5684 (t0) cc_final: 0.5401 (t0) REVERT: E 170 ARG cc_start: 0.5124 (mmt90) cc_final: 0.4539 (tpp-160) REVERT: E 171 ASP cc_start: 0.5097 (t0) cc_final: 0.4888 (m-30) REVERT: E 183 PHE cc_start: 0.6501 (m-80) cc_final: 0.6130 (m-80) REVERT: E 188 MET cc_start: 0.5329 (mtp) cc_final: 0.4947 (mtt) REVERT: E 198 GLU cc_start: 0.4513 (tt0) cc_final: 0.4139 (pt0) REVERT: F 5 HIS cc_start: 0.4495 (t-170) cc_final: 0.4278 (t70) REVERT: F 24 SER cc_start: 0.3948 (t) cc_final: 0.3733 (m) REVERT: F 25 VAL cc_start: 0.5105 (p) cc_final: 0.4876 (m) REVERT: F 27 GLN cc_start: 0.4793 (mt0) cc_final: 0.4531 (mt0) REVERT: F 30 ARG cc_start: 0.4591 (ptt-90) cc_final: 0.4065 (ptm160) REVERT: F 44 ILE cc_start: 0.3821 (pt) cc_final: 0.3581 (pp) REVERT: F 50 LEU cc_start: 0.4466 (tp) cc_final: 0.4209 (tm) REVERT: F 69 LYS cc_start: 0.5720 (mptt) cc_final: 0.5163 (mtmm) REVERT: F 72 LYS cc_start: 0.5154 (mmtp) cc_final: 0.4643 (mtmt) REVERT: F 83 TYR cc_start: 0.3822 (t80) cc_final: 0.3463 (m-80) REVERT: F 94 GLU cc_start: 0.4369 (mp0) cc_final: 0.3870 (tt0) REVERT: F 96 MET cc_start: 0.6069 (ttp) cc_final: 0.5697 (ttp) REVERT: F 100 PHE cc_start: 0.5527 (t80) cc_final: 0.5246 (t80) REVERT: F 104 ILE cc_start: 0.5340 (pt) cc_final: 0.5093 (mp) REVERT: F 125 ARG cc_start: 0.4050 (mmt90) cc_final: 0.3685 (mtp-110) REVERT: F 128 TYR cc_start: 0.6156 (t80) cc_final: 0.5676 (t80) REVERT: F 130 MET cc_start: 0.5514 (ptm) cc_final: 0.5206 (ppp) REVERT: F 133 ARG cc_start: 0.4090 (mtt-85) cc_final: 0.3875 (mtm180) REVERT: F 167 ARG cc_start: 0.4156 (mtt90) cc_final: 0.3634 (ttp80) REVERT: F 178 ARG cc_start: 0.2369 (mtm-85) cc_final: 0.2076 (mtt180) REVERT: G 85 LYS cc_start: 0.4342 (OUTLIER) cc_final: 0.3940 (mmtm) REVERT: G 86 LYS cc_start: 0.4506 (ttmm) cc_final: 0.4088 (tptp) REVERT: G 92 VAL cc_start: 0.4578 (p) cc_final: 0.4366 (t) REVERT: G 99 LYS cc_start: 0.4264 (mtmm) cc_final: 0.3949 (tptt) REVERT: G 115 HIS cc_start: 0.4836 (t-90) cc_final: 0.4551 (t-170) REVERT: G 132 VAL cc_start: 0.4931 (t) cc_final: 0.4565 (p) REVERT: G 134 LYS cc_start: 0.4755 (mttm) cc_final: 0.3968 (tmmt) REVERT: G 138 LYS cc_start: 0.5067 (tttt) cc_final: 0.4710 (ttpt) REVERT: G 143 GLN cc_start: 0.6363 (tp-100) cc_final: 0.6044 (tp40) REVERT: G 149 ARG cc_start: 0.6050 (ttt-90) cc_final: 0.5798 (ttt-90) REVERT: G 160 LYS cc_start: 0.5246 (mtpp) cc_final: 0.4949 (mtmt) REVERT: G 163 ARG cc_start: 0.5945 (ptp-170) cc_final: 0.5650 (ptp-170) REVERT: H 1 MET cc_start: 0.4020 (tpp) cc_final: 0.3704 (ttm) REVERT: H 22 LYS cc_start: 0.5981 (mmtp) cc_final: 0.5611 (mttp) REVERT: J 11 VAL cc_start: 0.5148 (t) cc_final: 0.4881 (m) REVERT: J 16 TYR cc_start: 0.7044 (m-80) cc_final: 0.6812 (m-80) REVERT: J 19 ASP cc_start: 0.6771 (t0) cc_final: 0.6509 (t0) REVERT: J 41 LYS cc_start: 0.6674 (mttt) cc_final: 0.6078 (mttm) REVERT: J 69 ARG cc_start: 0.6514 (ttm-80) cc_final: 0.5858 (mtt-85) REVERT: J 85 LYS cc_start: 0.6710 (mttm) cc_final: 0.6090 (mmtm) REVERT: J 90 GLU cc_start: 0.6191 (pt0) cc_final: 0.5427 (mt-10) REVERT: J 95 ARG cc_start: 0.4996 (ttm-80) cc_final: 0.4596 (ttp-170) REVERT: J 96 ARG cc_start: 0.4714 (ttt-90) cc_final: 0.4219 (mmm-85) REVERT: J 99 ARG cc_start: 0.6102 (mmm160) cc_final: 0.5674 (mmp-170) REVERT: J 140 LEU cc_start: 0.5528 (tp) cc_final: 0.5326 (tp) REVERT: K 4 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6670 (mt-10) REVERT: K 7 MET cc_start: 0.7372 (mmt) cc_final: 0.6660 (mmm) REVERT: K 12 ASP cc_start: 0.6692 (p0) cc_final: 0.6464 (p0) REVERT: K 17 ARG cc_start: 0.5940 (tpp-160) cc_final: 0.5581 (mmt90) REVERT: K 18 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.5738 (tpp80) REVERT: K 20 MET cc_start: 0.7586 (ttp) cc_final: 0.7279 (ttm) REVERT: K 53 LYS cc_start: 0.5671 (pttp) cc_final: 0.4872 (tptp) REVERT: K 54 LYS cc_start: 0.7002 (tttt) cc_final: 0.6700 (tttp) REVERT: K 71 ARG cc_start: 0.6448 (mmt90) cc_final: 0.6160 (mmt90) REVERT: K 75 SER cc_start: 0.6773 (m) cc_final: 0.6494 (p) REVERT: K 88 ASN cc_start: 0.5797 (t0) cc_final: 0.5447 (t0) REVERT: K 93 GLN cc_start: 0.5263 (mm-40) cc_final: 0.4916 (tp40) REVERT: K 98 ARG cc_start: 0.5934 (mmt180) cc_final: 0.5101 (mmm-85) REVERT: K 114 LYS cc_start: 0.5222 (tptt) cc_final: 0.4989 (tttm) REVERT: K 121 GLU cc_start: 0.6216 (tt0) cc_final: 0.5904 (tt0) REVERT: L 2 ARG cc_start: 0.5038 (mmm-85) cc_final: 0.4809 (mtp180) REVERT: L 14 LYS cc_start: 0.5664 (tttt) cc_final: 0.5337 (ttpt) REVERT: L 70 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6480 (ttpt) REVERT: L 76 GLU cc_start: 0.6135 (pt0) cc_final: 0.5745 (pt0) REVERT: L 78 ARG cc_start: 0.5643 (mtp-110) cc_final: 0.5351 (mtp85) REVERT: L 100 ILE cc_start: 0.6404 (mm) cc_final: 0.6192 (mm) REVERT: L 103 ILE cc_start: 0.5876 (mt) cc_final: 0.5657 (pp) REVERT: L 104 GLN cc_start: 0.6351 (mm110) cc_final: 0.6120 (mm-40) REVERT: L 123 ARG cc_start: 0.4652 (ttm-80) cc_final: 0.4077 (mtt90) REVERT: M 5 LYS cc_start: 0.6119 (mtpt) cc_final: 0.5855 (mttp) REVERT: M 6 ARG cc_start: 0.5362 (ttt-90) cc_final: 0.4796 (mtp85) REVERT: M 30 SER cc_start: 0.6931 (m) cc_final: 0.6512 (p) REVERT: M 55 ARG cc_start: 0.6450 (tpp80) cc_final: 0.6109 (tpp80) REVERT: M 59 ARG cc_start: 0.6452 (ttp80) cc_final: 0.6148 (mtm180) REVERT: M 60 GLN cc_start: 0.5101 (mm110) cc_final: 0.4867 (mp10) REVERT: M 106 ASP cc_start: 0.6531 (t0) cc_final: 0.6203 (t70) REVERT: M 118 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5600 (tttp) REVERT: M 133 LYS cc_start: 0.5595 (ttpp) cc_final: 0.5207 (ttmm) REVERT: N 22 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6917 (ttp80) REVERT: N 24 MET cc_start: 0.7625 (ttm) cc_final: 0.7381 (ttm) REVERT: N 46 ARG cc_start: 0.6834 (mtm110) cc_final: 0.6496 (mtp180) REVERT: N 73 ASN cc_start: 0.6417 (m-40) cc_final: 0.5838 (m-40) REVERT: O 9 ARG cc_start: 0.5622 (ttp-110) cc_final: 0.5218 (ttp80) REVERT: O 10 ARG cc_start: 0.6260 (mtm110) cc_final: 0.6017 (mtm-85) REVERT: O 16 ARG cc_start: 0.5784 (mmp80) cc_final: 0.5238 (mmt-90) REVERT: O 17 LYS cc_start: 0.5256 (mmtp) cc_final: 0.4899 (tppt) REVERT: O 19 GLN cc_start: 0.5507 (tt0) cc_final: 0.5110 (tm-30) REVERT: O 26 LEU cc_start: 0.5981 (tp) cc_final: 0.5233 (mt) REVERT: O 31 THR cc_start: 0.6190 (m) cc_final: 0.5815 (p) REVERT: O 38 GLN cc_start: 0.7292 (pt0) cc_final: 0.6840 (pt0) REVERT: O 45 SER cc_start: 0.4524 (m) cc_final: 0.4231 (p) REVERT: O 46 GLU cc_start: 0.5202 (mm-30) cc_final: 0.4993 (mm-30) REVERT: O 76 LYS cc_start: 0.5170 (tttt) cc_final: 0.4922 (tttm) REVERT: O 91 SER cc_start: 0.6497 (m) cc_final: 0.5977 (t) REVERT: P 7 GLN cc_start: 0.5438 (tt0) cc_final: 0.4825 (mm-40) REVERT: P 63 LYS cc_start: 0.6756 (ttpt) cc_final: 0.6420 (ttmt) REVERT: P 65 SER cc_start: 0.5548 (t) cc_final: 0.5046 (p) REVERT: P 84 ILE cc_start: 0.6330 (mt) cc_final: 0.6123 (mt) REVERT: P 89 ARG cc_start: 0.5607 (mtm-85) cc_final: 0.5161 (mtp-110) REVERT: P 111 LYS cc_start: 0.6071 (mmmt) cc_final: 0.5657 (mttp) REVERT: P 112 GLU cc_start: 0.6162 (tt0) cc_final: 0.5665 (tm-30) REVERT: Q 11 ARG cc_start: 0.6126 (tpm170) cc_final: 0.5233 (ttp-110) REVERT: Q 19 LYS cc_start: 0.7196 (tttp) cc_final: 0.6955 (tttm) REVERT: Q 22 LYS cc_start: 0.6845 (mttm) cc_final: 0.6618 (ttmm) REVERT: Q 78 LYS cc_start: 0.6371 (mtpp) cc_final: 0.5931 (mtmp) REVERT: Q 87 SER cc_start: 0.5755 (t) cc_final: 0.5405 (m) REVERT: Q 89 GLU cc_start: 0.5259 (mt-10) cc_final: 0.4761 (mm-30) REVERT: Q 93 LYS cc_start: 0.6648 (ttpt) cc_final: 0.6390 (tttm) REVERT: Q 97 ASP cc_start: 0.7084 (t70) cc_final: 0.6880 (t0) REVERT: Q 103 LYS cc_start: 0.5711 (mmtt) cc_final: 0.4853 (mmmt) REVERT: R 6 GLN cc_start: 0.5905 (tt0) cc_final: 0.4891 (pp30) REVERT: R 13 ARG cc_start: 0.6585 (ttp80) cc_final: 0.6253 (ttp-170) REVERT: R 34 GLU cc_start: 0.5041 (mt-10) cc_final: 0.4761 (mp0) REVERT: R 53 PHE cc_start: 0.5829 (m-80) cc_final: 0.5392 (m-10) REVERT: R 60 LYS cc_start: 0.4753 (mttp) cc_final: 0.4463 (mmmt) REVERT: R 62 GLU cc_start: 0.4870 (tt0) cc_final: 0.4245 (tp30) REVERT: R 70 GLU cc_start: 0.6433 (mm-30) cc_final: 0.5918 (tt0) REVERT: R 84 ARG cc_start: 0.6718 (ttp-110) cc_final: 0.6462 (ttp-170) REVERT: R 85 LYS cc_start: 0.6605 (ptpt) cc_final: 0.6193 (ptmm) REVERT: R 86 GLN cc_start: 0.6702 (pt0) cc_final: 0.6079 (mt0) REVERT: S 1 MET cc_start: 0.3406 (tpp) cc_final: 0.3173 (tpt) REVERT: S 4 ILE cc_start: 0.6932 (mt) cc_final: 0.6424 (tt) REVERT: S 11 ARG cc_start: 0.5893 (mmt-90) cc_final: 0.5444 (mmm-85) REVERT: S 27 LYS cc_start: 0.6061 (mmtp) cc_final: 0.5816 (mtpp) REVERT: S 31 GLN cc_start: 0.5152 (mt0) cc_final: 0.4638 (tt0) REVERT: S 65 ASP cc_start: 0.2639 (t0) cc_final: 0.2283 (p0) REVERT: S 73 LYS cc_start: 0.6839 (mttt) cc_final: 0.5687 (mmtm) REVERT: S 78 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6554 (mt-10) REVERT: S 82 MET cc_start: 0.6646 (mtm) cc_final: 0.6335 (mtm) REVERT: S 86 MET cc_start: 0.6971 (tpt) cc_final: 0.6485 (tpp) REVERT: T 4 GLU cc_start: 0.4406 (mt-10) cc_final: 0.4036 (tt0) REVERT: T 5 GLU cc_start: 0.4537 (mp0) cc_final: 0.4186 (tt0) REVERT: T 24 MET cc_start: 0.4724 (mtp) cc_final: 0.4392 (mtt) REVERT: T 26 LYS cc_start: 0.4292 (ttpp) cc_final: 0.3875 (tptp) REVERT: T 28 ASN cc_start: 0.5669 (m-40) cc_final: 0.5350 (t0) REVERT: T 33 LYS cc_start: 0.6350 (ttmt) cc_final: 0.6055 (mtpp) REVERT: T 39 THR cc_start: 0.6590 (m) cc_final: 0.6058 (p) REVERT: T 42 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6129 (mt-10) REVERT: T 56 GLU cc_start: 0.5464 (tp30) cc_final: 0.5105 (tp30) REVERT: T 69 ARG cc_start: 0.4862 (ptt-90) cc_final: 0.4560 (mtm110) REVERT: T 73 ARG cc_start: 0.3441 (tpt170) cc_final: 0.3018 (ttp-110) REVERT: U 10 GLU cc_start: 0.4716 (tm-30) cc_final: 0.4004 (mt-10) REVERT: U 19 LYS cc_start: 0.4963 (ttmt) cc_final: 0.4690 (ttpp) REVERT: U 26 LYS cc_start: 0.5145 (mmmt) cc_final: 0.4659 (mtpt) REVERT: U 31 SER cc_start: 0.4437 (p) cc_final: 0.4136 (t) REVERT: U 46 GLN cc_start: 0.5023 (pt0) cc_final: 0.4661 (tt0) REVERT: U 62 GLU cc_start: 0.5064 (mp0) cc_final: 0.3988 (tp30) REVERT: U 69 ASN cc_start: 0.7198 (m-40) cc_final: 0.6758 (m-40) REVERT: U 82 ARG cc_start: 0.5759 (mtm110) cc_final: 0.5497 (mtm-85) REVERT: U 95 PHE cc_start: 0.5831 (p90) cc_final: 0.5062 (p90) REVERT: U 96 PHE cc_start: 0.5591 (m-80) cc_final: 0.5374 (m-10) REVERT: V 11 GLU cc_start: 0.4597 (pt0) cc_final: 0.3957 (mt-10) REVERT: V 24 ASN cc_start: 0.5317 (t0) cc_final: 0.5012 (m-40) REVERT: V 25 LYS cc_start: 0.6217 (mttm) cc_final: 0.5885 (mtpp) REVERT: V 38 LEU cc_start: 0.5810 (tp) cc_final: 0.5478 (tp) REVERT: V 48 MET cc_start: 0.5687 (tpt) cc_final: 0.5083 (tpt) REVERT: V 51 GLN cc_start: 0.5541 (pp30) cc_final: 0.5121 (pp30) REVERT: V 75 GLN cc_start: 0.5535 (tp40) cc_final: 0.5235 (tp-100) REVERT: V 82 TYR cc_start: 0.6328 (p90) cc_final: 0.5975 (p90) REVERT: V 83 LYS cc_start: 0.6203 (mttm) cc_final: 0.5994 (mttm) REVERT: V 93 ARG cc_start: 0.5655 (mtt90) cc_final: 0.5302 (mtt90) REVERT: W 17 GLU cc_start: 0.6412 (tt0) cc_final: 0.6120 (tt0) REVERT: W 24 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6762 (mmtp) REVERT: W 29 GLU cc_start: 0.6812 (tt0) cc_final: 0.6272 (mt-10) REVERT: W 39 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6051 (mmm160) REVERT: W 44 LYS cc_start: 0.6769 (tttt) cc_final: 0.6482 (mtpt) REVERT: W 55 ARG cc_start: 0.7122 (ptm-80) cc_final: 0.6829 (ptm-80) REVERT: W 62 LYS cc_start: 0.7021 (mttt) cc_final: 0.6506 (mtpp) REVERT: W 66 LYS cc_start: 0.6467 (mttt) cc_final: 0.5950 (mtpt) REVERT: W 68 LYS cc_start: 0.7104 (tptp) cc_final: 0.6874 (tttp) REVERT: W 72 LYS cc_start: 0.5631 (mmmt) cc_final: 0.5201 (mmtm) REVERT: W 75 LYS cc_start: 0.5434 (mttt) cc_final: 0.5220 (mtpt) REVERT: W 78 LYS cc_start: 0.6440 (mttt) cc_final: 0.6004 (mtmm) REVERT: W 83 GLU cc_start: 0.5524 (mt-10) cc_final: 0.4858 (mm-30) REVERT: X 56 MET cc_start: 0.6910 (mtp) cc_final: 0.6708 (mtm) REVERT: X 64 ILE cc_start: 0.6343 (tp) cc_final: 0.6129 (tp) REVERT: X 65 ASP cc_start: 0.4909 (m-30) cc_final: 0.4489 (p0) REVERT: Y 1 MET cc_start: 0.3071 (mmm) cc_final: 0.2808 (tpp) REVERT: Y 27 ASN cc_start: 0.5182 (m110) cc_final: 0.4704 (m110) REVERT: Y 29 ARG cc_start: 0.5226 (mtm-85) cc_final: 0.4700 (ttm-80) REVERT: Y 30 MET cc_start: 0.5375 (mmm) cc_final: 0.5052 (mmm) REVERT: Y 57 LEU cc_start: 0.5886 (mt) cc_final: 0.5431 (mt) REVERT: Y 59 GLU cc_start: 0.4168 (pt0) cc_final: 0.3505 (tp30) REVERT: Z 30 ARG cc_start: 0.6443 (mtt-85) cc_final: 0.6153 (mtt-85) REVERT: Z 31 ARG cc_start: 0.6052 (ptt-90) cc_final: 0.5770 (ptp90) REVERT: Z 56 LYS cc_start: 0.5672 (tmtt) cc_final: 0.5300 (ttpt) REVERT: a 37 LYS cc_start: 0.6052 (mtmm) cc_final: 0.5652 (mtmt) REVERT: a 46 ASP cc_start: 0.4957 (t0) cc_final: 0.4740 (t70) REVERT: a 52 ARG cc_start: 0.5098 (ptp90) cc_final: 0.4534 (ptt90) REVERT: a 53 LYS cc_start: 0.6149 (tptm) cc_final: 0.5898 (tptm) REVERT: b 10 LYS cc_start: 0.4727 (mptt) cc_final: 0.3994 (mtpm) REVERT: b 25 LYS cc_start: 0.6916 (ttpt) cc_final: 0.6668 (ttpt) REVERT: b 32 GLU cc_start: 0.3802 (mp0) cc_final: 0.3346 (tt0) REVERT: b 33 LYS cc_start: 0.5379 (mmtt) cc_final: 0.4905 (mmmm) REVERT: b 35 GLU cc_start: 0.5728 (mt-10) cc_final: 0.5166 (tt0) REVERT: b 38 LYS cc_start: 0.6733 (mtpt) cc_final: 0.6476 (mtpp) REVERT: b 44 ARG cc_start: 0.5892 (mtp180) cc_final: 0.4416 (mtp85) REVERT: b 45 GLN cc_start: 0.6234 (tp40) cc_final: 0.5914 (mm-40) REVERT: b 47 VAL cc_start: 0.6855 (p) cc_final: 0.6567 (m) REVERT: b 50 LYS cc_start: 0.5934 (ttmt) cc_final: 0.5708 (mttp) REVERT: c 12 ARG cc_start: 0.7010 (ttp80) cc_final: 0.6457 (ttt90) REVERT: c 25 LYS cc_start: 0.6524 (tptm) cc_final: 0.6304 (tppt) REVERT: c 29 GLN cc_start: 0.6888 (mt0) cc_final: 0.5848 (mm110) REVERT: c 41 ARG cc_start: 0.5640 (ptp90) cc_final: 0.4905 (ttp80) REVERT: d 16 LYS cc_start: 0.6093 (tptm) cc_final: 0.5771 (tmtt) REVERT: d 51 SER cc_start: 0.6688 (p) cc_final: 0.6483 (p) REVERT: j 49 MET cc_start: 0.3837 (mtp) cc_final: 0.3521 (mtm) REVERT: j 50 PHE cc_start: 0.2990 (OUTLIER) cc_final: 0.2730 (p90) REVERT: j 96 TRP cc_start: 0.5872 (t-100) cc_final: 0.5464 (t-100) REVERT: j 105 LYS cc_start: 0.5103 (tttt) cc_final: 0.4672 (tptp) REVERT: j 143 LYS cc_start: 0.3251 (tttp) cc_final: 0.2944 (mtmp) REVERT: j 169 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5492 (mm-30) REVERT: j 186 ILE cc_start: 0.5515 (tt) cc_final: 0.5264 (mt) REVERT: j 192 ASP cc_start: 0.5061 (t0) cc_final: 0.4730 (t70) REVERT: j 214 LEU cc_start: 0.3814 (tp) cc_final: 0.3609 (tp) REVERT: m 30 ILE cc_start: 0.6301 (tp) cc_final: 0.6031 (mm) REVERT: m 43 ASN cc_start: 0.4823 (t0) cc_final: 0.4455 (m-40) REVERT: m 45 ARG cc_start: 0.4963 (mmm-85) cc_final: 0.4263 (mmm-85) REVERT: m 48 PHE cc_start: 0.6337 (p90) cc_final: 0.6101 (p90) REVERT: m 55 GLU cc_start: 0.4847 (mm-30) cc_final: 0.4346 (pt0) REVERT: m 61 GLN cc_start: 0.5670 (tt0) cc_final: 0.5212 (tp40) REVERT: m 62 LYS cc_start: 0.5849 (mttt) cc_final: 0.5497 (mttt) REVERT: m 64 MET cc_start: 0.5079 (mmt) cc_final: 0.4831 (mmt) REVERT: m 65 GLU cc_start: 0.5542 (tt0) cc_final: 0.5135 (tm-30) REVERT: m 66 LYS cc_start: 0.4787 (mttm) cc_final: 0.4466 (mttm) REVERT: m 71 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.4919 (ttp) REVERT: m 73 ASN cc_start: 0.4919 (m-40) cc_final: 0.4687 (m-40) REVERT: m 83 HIS cc_start: 0.6390 (p90) cc_final: 0.6128 (p90) REVERT: m 93 ARG cc_start: 0.5289 (mpp-170) cc_final: 0.5032 (mtt90) REVERT: m 124 LEU cc_start: 0.6001 (mt) cc_final: 0.5746 (mt) REVERT: m 138 ARG cc_start: 0.6487 (mtp85) cc_final: 0.5728 (mtt-85) REVERT: m 152 MET cc_start: 0.3760 (mmt) cc_final: 0.3546 (mtp) REVERT: n 21 MET cc_start: 0.4181 (mtm) cc_final: 0.3967 (mtt) REVERT: n 22 ILE cc_start: 0.4072 (mt) cc_final: 0.3856 (mt) REVERT: n 38 ARG cc_start: 0.5098 (ttt-90) cc_final: 0.4819 (ttt180) REVERT: n 46 GLN cc_start: 0.4756 (tp-100) cc_final: 0.4548 (tp40) REVERT: n 78 PHE cc_start: 0.5400 (m-80) cc_final: 0.4931 (m-80) REVERT: n 90 MET cc_start: 0.5743 (mtm) cc_final: 0.5539 (mtm) REVERT: n 91 ARG cc_start: 0.5733 (ttt180) cc_final: 0.5399 (mmm160) REVERT: o 4 ARG cc_start: 0.4193 (ttt180) cc_final: 0.3967 (ttp-170) REVERT: o 5 ARG cc_start: 0.2736 (OUTLIER) cc_final: 0.2251 (ptm-80) REVERT: o 12 ILE cc_start: 0.3540 (pt) cc_final: 0.3309 (tt) REVERT: o 13 LEU cc_start: 0.3879 (mp) cc_final: 0.3142 (pp) REVERT: o 37 SER cc_start: 0.5565 (m) cc_final: 0.5224 (p) REVERT: o 40 GLU cc_start: 0.5075 (pt0) cc_final: 0.4563 (mt-10) REVERT: o 58 GLU cc_start: 0.2045 (mm-30) cc_final: 0.1829 (pm20) REVERT: o 74 GLU cc_start: 0.4937 (pt0) cc_final: 0.4687 (pt0) REVERT: o 101 MET cc_start: 0.5901 (mtm) cc_final: 0.5697 (mtm) REVERT: o 106 GLU cc_start: 0.5290 (tt0) cc_final: 0.4649 (mm-30) REVERT: o 111 ARG cc_start: 0.3306 (mtp85) cc_final: 0.2940 (mtp85) REVERT: o 123 GLU cc_start: 0.4458 (tp30) cc_final: 0.3514 (tm-30) REVERT: o 136 LYS cc_start: 0.3731 (tttm) cc_final: 0.3377 (mmtp) REVERT: o 144 MET cc_start: 0.5185 (mmm) cc_final: 0.4790 (mtp) REVERT: o 146 GLU cc_start: 0.4324 (mm-30) cc_final: 0.3841 (tm-30) REVERT: p 9 ASP cc_start: 0.6107 (t70) cc_final: 0.5783 (t70) REVERT: p 15 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6787 (ttp80) REVERT: p 21 ASN cc_start: 0.5665 (m110) cc_final: 0.5313 (m110) REVERT: p 27 MET cc_start: 0.5895 (ptp) cc_final: 0.5602 (ptp) REVERT: p 28 PRO cc_start: 0.4925 (Cg_exo) cc_final: 0.4654 (Cg_endo) REVERT: p 51 VAL cc_start: 0.4257 (OUTLIER) cc_final: 0.3943 (t) REVERT: p 108 LYS cc_start: 0.4067 (mmtp) cc_final: 0.3814 (mptm) REVERT: p 111 MET cc_start: 0.5708 (ptp) cc_final: 0.5501 (ptp) REVERT: q 18 ARG cc_start: 0.4826 (mtm110) cc_final: 0.4123 (mtm110) REVERT: q 65 ILE cc_start: 0.4417 (mt) cc_final: 0.4158 (mp) REVERT: q 112 GLU cc_start: 0.6215 (tt0) cc_final: 0.5596 (tt0) REVERT: q 119 ARG cc_start: 0.4669 (mtm110) cc_final: 0.4235 (mtt180) REVERT: q 124 ARG cc_start: 0.6003 (ttm-80) cc_final: 0.5683 (mtp85) REVERT: s 27 PHE cc_start: 0.5925 (m-80) cc_final: 0.5375 (m-80) REVERT: s 40 ASN cc_start: 0.5555 (m-40) cc_final: 0.5249 (m110) REVERT: s 44 TRP cc_start: 0.7084 (p-90) cc_final: 0.6863 (p-90) REVERT: s 52 PHE cc_start: 0.5573 (m-80) cc_final: 0.5064 (m-80) REVERT: s 56 ARG cc_start: 0.4581 (mtm-85) cc_final: 0.4307 (mtm-85) REVERT: s 57 LYS cc_start: 0.6159 (ttpp) cc_final: 0.5905 (ttmt) REVERT: s 69 ARG cc_start: 0.4214 (mtp-110) cc_final: 0.3967 (mtp-110) REVERT: t 20 ASN cc_start: 0.4248 (p0) cc_final: 0.3921 (t0) REVERT: t 29 GLN cc_start: 0.5158 (mp10) cc_final: 0.4222 (mp10) REVERT: t 31 ARG cc_start: 0.4139 (ptt90) cc_final: 0.3359 (ptt180) REVERT: t 36 ARG cc_start: 0.3737 (OUTLIER) cc_final: 0.3198 (ptm160) REVERT: t 54 ARG cc_start: 0.3976 (ttp-110) cc_final: 0.3470 (mtp180) REVERT: t 95 TYR cc_start: 0.5324 (m-80) cc_final: 0.4830 (m-80) REVERT: u 19 LEU cc_start: 0.5388 (mt) cc_final: 0.5153 (mt) REVERT: u 62 LYS cc_start: 0.3290 (mttt) cc_final: 0.2893 (mtpm) REVERT: u 70 ARG cc_start: 0.4603 (mtt-85) cc_final: 0.4196 (mtm-85) REVERT: u 72 GLU cc_start: 0.4510 (mt-10) cc_final: 0.4086 (tm-30) REVERT: u 79 ARG cc_start: 0.5090 (ttp80) cc_final: 0.4187 (ttm170) REVERT: u 93 ARG cc_start: 0.4265 (mtp85) cc_final: 0.3991 (mmt90) REVERT: u 97 VAL cc_start: 0.5129 (t) cc_final: 0.4883 (m) REVERT: v 3 LYS cc_start: 0.5833 (mtmt) cc_final: 0.5561 (mtmt) REVERT: v 24 ARG cc_start: 0.3360 (OUTLIER) cc_final: 0.3021 (tpm170) REVERT: v 86 GLU cc_start: 0.5426 (mm-30) cc_final: 0.5153 (mt-10) REVERT: v 89 MET cc_start: 0.5875 (mmt) cc_final: 0.5494 (mmp) REVERT: v 90 ARG cc_start: 0.5746 (mtt90) cc_final: 0.4976 (mtt90) REVERT: w 14 GLU cc_start: 0.3856 (mt-10) cc_final: 0.3584 (tt0) REVERT: w 21 ASP cc_start: 0.4302 (t70) cc_final: 0.3865 (t70) REVERT: w 24 SER cc_start: 0.5269 (t) cc_final: 0.4949 (t) REVERT: w 28 GLN cc_start: 0.5441 (mt0) cc_final: 0.5236 (mt0) REVERT: w 35 GLN cc_start: 0.5205 (tp40) cc_final: 0.3728 (mt0) REVERT: w 56 LEU cc_start: 0.6443 (tp) cc_final: 0.6120 (tm) REVERT: w 58 ARG cc_start: 0.6234 (ttt-90) cc_final: 0.5889 (ttp80) REVERT: w 59 MET cc_start: 0.7045 (mtt) cc_final: 0.6703 (mtm) REVERT: y 12 VAL cc_start: 0.3539 (t) cc_final: 0.3236 (m) REVERT: y 37 PHE cc_start: 0.6110 (m-80) cc_final: 0.5886 (m-80) REVERT: z 29 LEU cc_start: 0.5553 (mp) cc_final: 0.5294 (mp) REVERT: z 48 ARG cc_start: 0.5236 (mmt-90) cc_final: 0.4913 (mmm160) REVERT: z 57 ARG cc_start: 0.6435 (mtt90) cc_final: 0.6139 (mtt180) REVERT: z 66 SER cc_start: 0.7012 (OUTLIER) cc_final: 0.6745 (m) REVERT: 1 66 MET cc_start: 0.4648 (mtt) cc_final: 0.3862 (mtm) REVERT: 2 8 LYS cc_start: 0.4619 (mttt) cc_final: 0.4276 (mttm) REVERT: 2 29 ARG cc_start: 0.4634 (mtt180) cc_final: 0.4383 (mtm-85) REVERT: 3 32 VAL cc_start: 0.5429 (t) cc_final: 0.4993 (m) REVERT: 3 36 GLU cc_start: 0.6522 (tt0) cc_final: 0.6053 (mt-10) REVERT: 3 39 GLU cc_start: 0.5537 (tm-30) cc_final: 0.4783 (pp20) REVERT: 3 40 LYS cc_start: 0.5987 (tptt) cc_final: 0.5329 (mttt) REVERT: 3 46 LYS cc_start: 0.4878 (ttmt) cc_final: 0.4528 (ttmt) REVERT: e 1 MET cc_start: 0.7059 (tpp) cc_final: 0.6532 (tpt) REVERT: e 15 LYS cc_start: 0.6259 (tttm) cc_final: 0.5529 (tptt) REVERT: e 28 SER cc_start: 0.5177 (p) cc_final: 0.4975 (m) outliers start: 36 outliers final: 9 residues processed: 1066 average time/residue: 2.3834 time to fit residues: 3540.7688 Evaluate side-chains 837 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 819 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 71 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 5 ARG Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 80 ILE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain z residue 66 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 789 optimal weight: 0.3980 chunk 708 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 478 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 732 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 445 optimal weight: 6.9990 chunk 545 optimal weight: 1.9990 chunk 849 optimal weight: 9.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 ASN D 150 GLN E 94 GLN E 163 ASN F 5 HIS G 38 ASN G 143 GLN H 2 GLN J 40 HIS K 3 GLN N 62 ASN O 38 GLN O 104 GLN P 3 ASN S 7 HIS S 15 GLN S 40 ASN S 60 HIS T 15 HIS T 59 ASN U 66 GLN V 12 GLN V 49 ASN X 16 ASN Y 15 ASN Y 39 GLN a 5 GLN a 6 ASN a 38 HIS c 13 ASN j 18 HIS j 19 GLN j 89 GLN j 103 ASN j 146 ASN j 170 HIS j 177 ASN j 178 ASN m 89 HIS n 55 HIS o 28 ASN o 148 ASN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 GLN v 43 ASN w 28 GLN w 37 ASN ** y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 52 GLN z 74 HIS 2 52 ASN 2 75 HIS e 35 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 152207 Z= 0.252 Angle : 0.800 9.458 229001 Z= 0.406 Chirality : 0.043 0.332 29444 Planarity : 0.007 0.152 11367 Dihedral : 23.690 179.909 79440 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Rotamer: Outliers : 2.78 % Allowed : 11.39 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 4751 helix: 0.27 (0.13), residues: 1524 sheet: -0.97 (0.16), residues: 932 loop : -0.87 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 248 HIS 0.011 0.002 HIS a 19 PHE 0.030 0.003 PHE F 100 TYR 0.025 0.003 TYR S 38 ARG 0.011 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 839 time to evaluate : 5.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5884 (mttt) cc_final: 0.5147 (mptt) REVERT: C 13 ARG cc_start: 0.7255 (tpt170) cc_final: 0.6953 (mmm160) REVERT: C 68 LYS cc_start: 0.6772 (mttt) cc_final: 0.6527 (mttm) REVERT: C 100 GLU cc_start: 0.6398 (tt0) cc_final: 0.6063 (tt0) REVERT: C 111 LYS cc_start: 0.5173 (ptmm) cc_final: 0.4925 (ptpp) REVERT: C 125 LYS cc_start: 0.5349 (pttt) cc_final: 0.4925 (ptpt) REVERT: C 133 ARG cc_start: 0.5592 (ptt-90) cc_final: 0.4988 (ttm-80) REVERT: C 146 MET cc_start: 0.7107 (mtp) cc_final: 0.6760 (mtm) REVERT: C 163 GLN cc_start: 0.6770 (tt0) cc_final: 0.6210 (mt0) REVERT: C 181 MET cc_start: 0.6867 (mmm) cc_final: 0.6659 (mmm) REVERT: C 183 LYS cc_start: 0.5970 (mttt) cc_final: 0.5622 (mtpt) REVERT: C 185 GLU cc_start: 0.6316 (mt-10) cc_final: 0.6114 (mt-10) REVERT: C 194 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6463 (mt-10) REVERT: C 201 MET cc_start: 0.7048 (ptt) cc_final: 0.6789 (ptm) REVERT: C 203 ARG cc_start: 0.6062 (ptt180) cc_final: 0.5728 (ptp-110) REVERT: C 269 ARG cc_start: 0.5877 (ttp-170) cc_final: 0.5153 (ttp80) REVERT: D 17 GLU cc_start: 0.4155 (tt0) cc_final: 0.3896 (mp0) REVERT: D 39 ASP cc_start: 0.4907 (t0) cc_final: 0.4312 (m-30) REVERT: D 55 LYS cc_start: 0.5094 (ttmm) cc_final: 0.4767 (ttmt) REVERT: D 70 LYS cc_start: 0.4951 (tttt) cc_final: 0.4692 (tptt) REVERT: D 74 GLU cc_start: 0.4916 (tt0) cc_final: 0.4551 (mp0) REVERT: D 99 GLU cc_start: 0.5380 (tp30) cc_final: 0.4844 (pt0) REVERT: D 105 LYS cc_start: 0.5777 (mttt) cc_final: 0.5415 (mmmt) REVERT: D 128 ARG cc_start: 0.7012 (mtt90) cc_final: 0.6669 (mtt180) REVERT: D 131 ASP cc_start: 0.6928 (m-30) cc_final: 0.6502 (m-30) REVERT: D 190 LYS cc_start: 0.7213 (tttt) cc_final: 0.6542 (tttp) REVERT: E 22 ASP cc_start: 0.4063 (OUTLIER) cc_final: 0.3606 (p0) REVERT: E 57 LYS cc_start: 0.6303 (tttp) cc_final: 0.6099 (tptm) REVERT: E 61 ARG cc_start: 0.6981 (ptm160) cc_final: 0.6372 (ptt-90) REVERT: E 116 ASP cc_start: 0.4783 (OUTLIER) cc_final: 0.4545 (t0) REVERT: E 120 VAL cc_start: 0.5122 (t) cc_final: 0.4761 (p) REVERT: E 130 LYS cc_start: 0.4573 (mmtm) cc_final: 0.4038 (tppt) REVERT: E 141 MET cc_start: 0.3854 (mtp) cc_final: 0.3461 (ttt) REVERT: E 167 VAL cc_start: 0.5482 (t) cc_final: 0.4933 (m) REVERT: E 170 ARG cc_start: 0.4959 (mmt90) cc_final: 0.4607 (tpp80) REVERT: E 188 MET cc_start: 0.5247 (mtp) cc_final: 0.4911 (mtt) REVERT: F 25 VAL cc_start: 0.5037 (p) cc_final: 0.4768 (m) REVERT: F 63 GLN cc_start: 0.5893 (mt0) cc_final: 0.4944 (mt0) REVERT: F 69 LYS cc_start: 0.5561 (mptt) cc_final: 0.5161 (mppt) REVERT: F 83 TYR cc_start: 0.3845 (t80) cc_final: 0.3415 (m-10) REVERT: F 89 VAL cc_start: 0.6303 (OUTLIER) cc_final: 0.5926 (m) REVERT: F 100 PHE cc_start: 0.5708 (t80) cc_final: 0.5255 (t80) REVERT: F 125 ARG cc_start: 0.4007 (mmt90) cc_final: 0.3759 (mmt90) REVERT: F 128 TYR cc_start: 0.6232 (t80) cc_final: 0.6003 (t80) REVERT: F 130 MET cc_start: 0.5536 (ptm) cc_final: 0.5317 (ptp) REVERT: F 133 ARG cc_start: 0.4041 (mtt-85) cc_final: 0.3556 (mtp85) REVERT: G 71 LEU cc_start: 0.5111 (mt) cc_final: 0.4676 (mp) REVERT: G 85 LYS cc_start: 0.4144 (OUTLIER) cc_final: 0.3895 (tppt) REVERT: G 86 LYS cc_start: 0.4706 (ttmm) cc_final: 0.4229 (tptp) REVERT: G 88 GLN cc_start: 0.5021 (pt0) cc_final: 0.3918 (tm-30) REVERT: G 92 VAL cc_start: 0.4150 (p) cc_final: 0.3950 (t) REVERT: G 99 LYS cc_start: 0.4318 (mtmm) cc_final: 0.4040 (tptt) REVERT: G 132 VAL cc_start: 0.5196 (t) cc_final: 0.4725 (p) REVERT: G 143 GLN cc_start: 0.6201 (tp40) cc_final: 0.5876 (tp40) REVERT: G 149 ARG cc_start: 0.5839 (ttt-90) cc_final: 0.5556 (ttt-90) REVERT: G 160 LYS cc_start: 0.5346 (mtpp) cc_final: 0.5040 (mtmt) REVERT: H 1 MET cc_start: 0.4565 (tpp) cc_final: 0.4041 (ttm) REVERT: H 22 LYS cc_start: 0.5714 (mmtp) cc_final: 0.5332 (mttp) REVERT: J 19 ASP cc_start: 0.6533 (t0) cc_final: 0.6307 (t0) REVERT: J 23 LYS cc_start: 0.6429 (mmtm) cc_final: 0.6166 (mmtt) REVERT: J 31 GLU cc_start: 0.6415 (tp30) cc_final: 0.6002 (tm-30) REVERT: J 39 LYS cc_start: 0.6556 (mtpp) cc_final: 0.6266 (mmmm) REVERT: J 61 LYS cc_start: 0.6368 (mtmm) cc_final: 0.5626 (mmtt) REVERT: J 69 ARG cc_start: 0.6331 (ttm-80) cc_final: 0.5630 (mtt-85) REVERT: J 85 LYS cc_start: 0.6568 (mttm) cc_final: 0.5932 (mmtm) REVERT: J 90 GLU cc_start: 0.6243 (pt0) cc_final: 0.5311 (tp30) REVERT: J 95 ARG cc_start: 0.5088 (ttm-80) cc_final: 0.4675 (ttp-170) REVERT: J 96 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.3864 (ptp90) REVERT: J 99 ARG cc_start: 0.5913 (mmm160) cc_final: 0.5520 (mmp-170) REVERT: J 108 MET cc_start: 0.7860 (mtt) cc_final: 0.7640 (mtt) REVERT: J 129 GLU cc_start: 0.5374 (mm-30) cc_final: 0.4586 (mp0) REVERT: J 138 GLN cc_start: 0.5938 (OUTLIER) cc_final: 0.5340 (pt0) REVERT: K 20 MET cc_start: 0.7471 (ttp) cc_final: 0.7188 (ttm) REVERT: K 53 LYS cc_start: 0.5534 (pttp) cc_final: 0.4912 (tptp) REVERT: K 71 ARG cc_start: 0.6432 (mmt90) cc_final: 0.5814 (mmm160) REVERT: K 88 ASN cc_start: 0.5911 (t0) cc_final: 0.5521 (t0) REVERT: K 98 ARG cc_start: 0.6017 (mmt180) cc_final: 0.5171 (mtp180) REVERT: K 111 LYS cc_start: 0.4582 (mtpm) cc_final: 0.4323 (mtmp) REVERT: K 113 MET cc_start: 0.4591 (tpp) cc_final: 0.4348 (tpt) REVERT: K 114 LYS cc_start: 0.5120 (tptt) cc_final: 0.4889 (tttm) REVERT: K 121 GLU cc_start: 0.6358 (tt0) cc_final: 0.6011 (tt0) REVERT: L 14 LYS cc_start: 0.5463 (tttt) cc_final: 0.5179 (ttpt) REVERT: L 100 ILE cc_start: 0.6339 (mm) cc_final: 0.6127 (mt) REVERT: L 103 ILE cc_start: 0.5854 (mt) cc_final: 0.5648 (pp) REVERT: L 123 ARG cc_start: 0.4598 (ttm-80) cc_final: 0.4114 (mtt90) REVERT: M 5 LYS cc_start: 0.5994 (mtpt) cc_final: 0.5718 (mtpp) REVERT: M 6 ARG cc_start: 0.5354 (ttt-90) cc_final: 0.4797 (mtp85) REVERT: M 30 SER cc_start: 0.6842 (m) cc_final: 0.6407 (p) REVERT: M 55 ARG cc_start: 0.6353 (tpp80) cc_final: 0.6042 (ttt90) REVERT: M 59 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6089 (mtm180) REVERT: M 115 GLU cc_start: 0.5535 (mm-30) cc_final: 0.5174 (tt0) REVERT: M 118 LYS cc_start: 0.5956 (mmtm) cc_final: 0.5717 (ttmp) REVERT: M 127 LYS cc_start: 0.6012 (ttmt) cc_final: 0.5509 (tptp) REVERT: M 133 LYS cc_start: 0.5553 (ttpp) cc_final: 0.5193 (ttmm) REVERT: M 136 MET cc_start: 0.3217 (mtp) cc_final: 0.2795 (mtp) REVERT: N 73 ASN cc_start: 0.6442 (m-40) cc_final: 0.6021 (m-40) REVERT: N 117 ASP cc_start: 0.4398 (p0) cc_final: 0.4115 (t0) REVERT: O 16 ARG cc_start: 0.5750 (mmp80) cc_final: 0.5275 (mmt90) REVERT: O 17 LYS cc_start: 0.5183 (mmtp) cc_final: 0.4880 (tppt) REVERT: O 19 GLN cc_start: 0.5735 (tt0) cc_final: 0.5421 (tm-30) REVERT: O 26 LEU cc_start: 0.6045 (tp) cc_final: 0.5314 (mt) REVERT: O 31 THR cc_start: 0.6026 (m) cc_final: 0.5695 (p) REVERT: O 46 GLU cc_start: 0.5092 (mm-30) cc_final: 0.4305 (mt-10) REVERT: O 91 SER cc_start: 0.6216 (m) cc_final: 0.5727 (t) REVERT: P 6 LYS cc_start: 0.5274 (tptt) cc_final: 0.5028 (ttmt) REVERT: P 26 VAL cc_start: 0.6764 (OUTLIER) cc_final: 0.6547 (m) REVERT: P 33 VAL cc_start: 0.4703 (t) cc_final: 0.4496 (m) REVERT: P 65 SER cc_start: 0.5478 (t) cc_final: 0.5228 (p) REVERT: P 68 GLU cc_start: 0.5304 (tp30) cc_final: 0.5091 (tm-30) REVERT: P 89 ARG cc_start: 0.5680 (mtm-85) cc_final: 0.4991 (mtt-85) REVERT: P 111 LYS cc_start: 0.5890 (mmmt) cc_final: 0.5628 (mttp) REVERT: Q 11 ARG cc_start: 0.6253 (tpm170) cc_final: 0.5498 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6550 (mtpp) cc_final: 0.6120 (mtmt) REVERT: Q 84 LYS cc_start: 0.5594 (ttpp) cc_final: 0.5020 (mmtm) REVERT: Q 89 GLU cc_start: 0.5452 (mt-10) cc_final: 0.4879 (mm-30) REVERT: R 6 GLN cc_start: 0.5756 (tt0) cc_final: 0.5279 (pt0) REVERT: R 13 ARG cc_start: 0.6615 (ttp80) cc_final: 0.5987 (ttp-170) REVERT: R 34 GLU cc_start: 0.5141 (mt-10) cc_final: 0.4806 (mp0) REVERT: R 60 LYS cc_start: 0.4804 (mttp) cc_final: 0.4532 (mmmt) REVERT: R 62 GLU cc_start: 0.4840 (tt0) cc_final: 0.4122 (tp30) REVERT: R 70 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5818 (tt0) REVERT: R 86 GLN cc_start: 0.6777 (pt0) cc_final: 0.6098 (mt0) REVERT: S 11 ARG cc_start: 0.5865 (mmt-90) cc_final: 0.5415 (mmm-85) REVERT: S 12 SER cc_start: 0.6773 (t) cc_final: 0.6497 (p) REVERT: S 59 GLU cc_start: 0.4747 (mt-10) cc_final: 0.4506 (mm-30) REVERT: S 82 MET cc_start: 0.6583 (mtm) cc_final: 0.6309 (mtm) REVERT: S 86 MET cc_start: 0.6557 (tpt) cc_final: 0.6199 (tpp) REVERT: T 5 GLU cc_start: 0.4621 (mp0) cc_final: 0.4295 (tt0) REVERT: T 8 LEU cc_start: 0.6176 (mt) cc_final: 0.5900 (mt) REVERT: T 24 MET cc_start: 0.4728 (mtp) cc_final: 0.4517 (mtt) REVERT: T 26 LYS cc_start: 0.4269 (ttpp) cc_final: 0.3936 (mmtp) REVERT: T 33 LYS cc_start: 0.6177 (ttmt) cc_final: 0.5922 (mtpp) REVERT: T 56 GLU cc_start: 0.5368 (tp30) cc_final: 0.4864 (tp30) REVERT: T 69 ARG cc_start: 0.4804 (ptt-90) cc_final: 0.4299 (mtp85) REVERT: T 73 ARG cc_start: 0.3379 (tpt170) cc_final: 0.2945 (ttp-110) REVERT: U 9 ASP cc_start: 0.4779 (m-30) cc_final: 0.4026 (m-30) REVERT: U 19 LYS cc_start: 0.4858 (ttmt) cc_final: 0.4541 (ttpp) REVERT: U 26 LYS cc_start: 0.4738 (mmmt) cc_final: 0.4313 (mttm) REVERT: U 31 SER cc_start: 0.4640 (p) cc_final: 0.4416 (p) REVERT: U 46 GLN cc_start: 0.5276 (pt0) cc_final: 0.5051 (mt0) REVERT: U 62 GLU cc_start: 0.5165 (mp0) cc_final: 0.3943 (tp30) REVERT: U 95 PHE cc_start: 0.5712 (p90) cc_final: 0.4915 (p90) REVERT: U 96 PHE cc_start: 0.5682 (m-80) cc_final: 0.5347 (m-10) REVERT: V 11 GLU cc_start: 0.4930 (pt0) cc_final: 0.4306 (mt-10) REVERT: V 38 LEU cc_start: 0.5654 (tp) cc_final: 0.5361 (tp) REVERT: V 43 ASP cc_start: 0.5838 (t0) cc_final: 0.5191 (m-30) REVERT: V 48 MET cc_start: 0.5445 (tpt) cc_final: 0.4946 (tpt) REVERT: V 51 GLN cc_start: 0.5586 (pp30) cc_final: 0.5230 (pp30) REVERT: V 82 TYR cc_start: 0.6242 (p90) cc_final: 0.5928 (p90) REVERT: W 17 GLU cc_start: 0.6503 (tt0) cc_final: 0.6299 (tt0) REVERT: W 29 GLU cc_start: 0.6856 (tt0) cc_final: 0.6380 (mt-10) REVERT: W 39 ARG cc_start: 0.6574 (mtt-85) cc_final: 0.6000 (mtm180) REVERT: W 44 LYS cc_start: 0.6734 (tttt) cc_final: 0.6348 (mtpt) REVERT: W 62 LYS cc_start: 0.7034 (mttt) cc_final: 0.6508 (mtpp) REVERT: W 66 LYS cc_start: 0.6680 (mttt) cc_final: 0.6126 (mtpt) REVERT: W 72 LYS cc_start: 0.5571 (mmmt) cc_final: 0.5146 (mmtm) REVERT: W 75 LYS cc_start: 0.5083 (mttt) cc_final: 0.4871 (mtmt) REVERT: W 78 LYS cc_start: 0.6318 (mttt) cc_final: 0.5815 (mtmm) REVERT: W 83 GLU cc_start: 0.5466 (mt-10) cc_final: 0.4873 (mm-30) REVERT: Y 1 MET cc_start: 0.2692 (mmm) cc_final: 0.2337 (tpp) REVERT: Y 13 GLU cc_start: 0.4885 (mt-10) cc_final: 0.4408 (mm-30) REVERT: Y 27 ASN cc_start: 0.5167 (m110) cc_final: 0.4699 (m110) REVERT: Y 29 ARG cc_start: 0.5169 (mtm-85) cc_final: 0.4616 (ttm-80) REVERT: Y 30 MET cc_start: 0.5293 (mmm) cc_final: 0.5027 (mmm) REVERT: Y 46 VAL cc_start: 0.5598 (t) cc_final: 0.5337 (p) REVERT: Z 31 ARG cc_start: 0.5789 (ptt-90) cc_final: 0.5522 (ptp90) REVERT: Z 56 LYS cc_start: 0.5820 (tmtt) cc_final: 0.5499 (ttmt) REVERT: a 37 LYS cc_start: 0.5932 (mtmm) cc_final: 0.5579 (mmmt) REVERT: a 52 ARG cc_start: 0.5022 (ptp90) cc_final: 0.4599 (ptm-80) REVERT: b 7 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5484 (tt0) REVERT: b 10 LYS cc_start: 0.5157 (mptt) cc_final: 0.4447 (mtmt) REVERT: b 33 LYS cc_start: 0.5136 (mmtt) cc_final: 0.4786 (mmmm) REVERT: b 35 GLU cc_start: 0.5777 (mt-10) cc_final: 0.5470 (tt0) REVERT: b 44 ARG cc_start: 0.5751 (mtp180) cc_final: 0.4336 (mtp85) REVERT: b 45 GLN cc_start: 0.6265 (tp40) cc_final: 0.5974 (mm110) REVERT: b 50 LYS cc_start: 0.5618 (ttmt) cc_final: 0.5362 (mttt) REVERT: c 12 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6454 (ttt90) REVERT: c 25 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6054 (tmmt) REVERT: c 41 ARG cc_start: 0.5735 (ptp90) cc_final: 0.5021 (ttp80) REVERT: d 16 LYS cc_start: 0.6306 (tptm) cc_final: 0.5959 (tptt) REVERT: d 52 LYS cc_start: 0.4914 (ttpt) cc_final: 0.4694 (ttpp) REVERT: j 21 ARG cc_start: 0.3128 (OUTLIER) cc_final: 0.2462 (pmm-80) REVERT: j 50 PHE cc_start: 0.3035 (OUTLIER) cc_final: 0.2600 (p90) REVERT: j 105 LYS cc_start: 0.5007 (tttt) cc_final: 0.4591 (tptp) REVERT: j 141 LEU cc_start: 0.3110 (OUTLIER) cc_final: 0.2731 (mm) REVERT: j 143 LYS cc_start: 0.3341 (tttp) cc_final: 0.2902 (mmtm) REVERT: j 169 GLU cc_start: 0.5720 (mm-30) cc_final: 0.5447 (mm-30) REVERT: j 186 ILE cc_start: 0.5092 (OUTLIER) cc_final: 0.4887 (mt) REVERT: j 214 LEU cc_start: 0.4039 (tp) cc_final: 0.3803 (tp) REVERT: m 26 LYS cc_start: 0.5056 (tptp) cc_final: 0.4826 (ttpt) REVERT: m 30 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6120 (mm) REVERT: m 43 ASN cc_start: 0.4908 (t0) cc_final: 0.4556 (m-40) REVERT: m 55 GLU cc_start: 0.4469 (mm-30) cc_final: 0.3750 (pt0) REVERT: m 61 GLN cc_start: 0.5733 (tt0) cc_final: 0.5284 (tp40) REVERT: m 62 LYS cc_start: 0.5657 (mttt) cc_final: 0.5377 (mtpt) REVERT: m 64 MET cc_start: 0.5459 (mmt) cc_final: 0.5117 (mmt) REVERT: m 65 GLU cc_start: 0.5417 (tt0) cc_final: 0.5057 (tp30) REVERT: m 73 ASN cc_start: 0.4995 (m-40) cc_final: 0.4636 (m-40) REVERT: m 93 ARG cc_start: 0.5543 (mpp-170) cc_final: 0.5237 (mtt90) REVERT: m 142 ASP cc_start: 0.4018 (m-30) cc_final: 0.3705 (t0) REVERT: m 156 LYS cc_start: 0.4131 (mtmm) cc_final: 0.3619 (mtmm) REVERT: n 21 MET cc_start: 0.3920 (mtm) cc_final: 0.3492 (mtt) REVERT: n 52 ASN cc_start: 0.3741 (OUTLIER) cc_final: 0.3537 (m-40) REVERT: n 90 MET cc_start: 0.5860 (mtm) cc_final: 0.5346 (mtm) REVERT: o 74 GLU cc_start: 0.4924 (pt0) cc_final: 0.4672 (pt0) REVERT: o 106 GLU cc_start: 0.4929 (tt0) cc_final: 0.4369 (mm-30) REVERT: o 144 MET cc_start: 0.4787 (mmm) cc_final: 0.4462 (mtp) REVERT: o 146 GLU cc_start: 0.4289 (mm-30) cc_final: 0.3833 (tm-30) REVERT: p 28 PRO cc_start: 0.4707 (Cg_exo) cc_final: 0.4474 (Cg_endo) REVERT: p 40 LEU cc_start: 0.5247 (mt) cc_final: 0.5008 (mp) REVERT: q 19 VAL cc_start: 0.4513 (t) cc_final: 0.3966 (m) REVERT: q 65 ILE cc_start: 0.4331 (mt) cc_final: 0.4058 (mp) REVERT: q 119 ARG cc_start: 0.4838 (mtm110) cc_final: 0.4395 (mtt180) REVERT: q 124 ARG cc_start: 0.6112 (ttm-80) cc_final: 0.5577 (mtp180) REVERT: s 22 HIS cc_start: 0.6935 (m90) cc_final: 0.6643 (m90) REVERT: s 52 PHE cc_start: 0.5471 (m-80) cc_final: 0.4870 (m-80) REVERT: s 69 ARG cc_start: 0.4327 (mtp-110) cc_final: 0.4105 (mtp85) REVERT: t 20 ASN cc_start: 0.4288 (p0) cc_final: 0.4018 (t0) REVERT: t 29 GLN cc_start: 0.4768 (mp10) cc_final: 0.3882 (mp10) REVERT: t 54 ARG cc_start: 0.3766 (ttp-110) cc_final: 0.3333 (mtp180) REVERT: t 75 GLN cc_start: 0.1665 (OUTLIER) cc_final: 0.1422 (tm-30) REVERT: t 82 ILE cc_start: 0.4825 (OUTLIER) cc_final: 0.4384 (pt) REVERT: t 95 TYR cc_start: 0.5247 (m-80) cc_final: 0.4908 (m-80) REVERT: u 70 ARG cc_start: 0.4334 (mtt-85) cc_final: 0.4036 (mtm-85) REVERT: u 72 GLU cc_start: 0.4422 (mt-10) cc_final: 0.3714 (tp30) REVERT: u 79 ARG cc_start: 0.5024 (ttp80) cc_final: 0.4805 (ttt-90) REVERT: u 81 MET cc_start: 0.4941 (mtt) cc_final: 0.4495 (mmm) REVERT: u 93 ARG cc_start: 0.4279 (mtp85) cc_final: 0.4011 (mmt90) REVERT: v 6 MET cc_start: 0.5591 (mmm) cc_final: 0.5338 (mmm) REVERT: v 24 ARG cc_start: 0.3295 (OUTLIER) cc_final: 0.2762 (tpm170) REVERT: v 47 LYS cc_start: 0.3661 (mmtm) cc_final: 0.2722 (ptmm) REVERT: v 89 MET cc_start: 0.5974 (mmt) cc_final: 0.5519 (mmp) REVERT: v 90 ARG cc_start: 0.5777 (mtt90) cc_final: 0.4918 (mtt90) REVERT: w 53 ARG cc_start: 0.6628 (ttm-80) cc_final: 0.6428 (ttm110) REVERT: w 56 LEU cc_start: 0.6370 (tp) cc_final: 0.6112 (tm) REVERT: w 58 ARG cc_start: 0.6057 (ttt-90) cc_final: 0.5774 (ttp80) REVERT: w 59 MET cc_start: 0.6876 (mtt) cc_final: 0.6553 (mtm) REVERT: y 37 PHE cc_start: 0.6064 (m-80) cc_final: 0.5692 (m-80) REVERT: y 40 ARG cc_start: 0.3879 (mmp-170) cc_final: 0.3594 (mmm160) REVERT: z 38 LYS cc_start: 0.5627 (mtpp) cc_final: 0.5412 (mtmm) REVERT: z 61 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5027 (mtp180) REVERT: 1 49 ILE cc_start: 0.3918 (OUTLIER) cc_final: 0.3588 (mp) REVERT: 1 66 MET cc_start: 0.4625 (mtt) cc_final: 0.3908 (mtt) REVERT: 2 8 LYS cc_start: 0.4643 (mttt) cc_final: 0.4427 (mttm) REVERT: 3 32 VAL cc_start: 0.5219 (t) cc_final: 0.4698 (m) REVERT: 3 36 GLU cc_start: 0.6533 (tt0) cc_final: 0.6185 (mt-10) REVERT: 3 39 GLU cc_start: 0.5810 (tm-30) cc_final: 0.5074 (pp20) REVERT: 3 40 LYS cc_start: 0.5940 (tptt) cc_final: 0.5250 (mttt) REVERT: 3 46 LYS cc_start: 0.4821 (ttmt) cc_final: 0.4519 (ttmt) REVERT: e 8 LYS cc_start: 0.6193 (mtpt) cc_final: 0.5722 (ptpt) REVERT: e 15 LYS cc_start: 0.6219 (tttm) cc_final: 0.5522 (tptt) REVERT: e 30 GLU cc_start: 0.5101 (OUTLIER) cc_final: 0.4890 (mm-30) outliers start: 110 outliers final: 45 residues processed: 906 average time/residue: 2.3621 time to fit residues: 2997.8945 Evaluate side-chains 814 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 748 time to evaluate : 5.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 78 GLU Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 186 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 71 MET Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 49 ILE Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 471 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 706 optimal weight: 20.0000 chunk 578 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 850 optimal weight: 9.9990 chunk 918 optimal weight: 20.0000 chunk 757 optimal weight: 5.9990 chunk 843 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN O 38 GLN O 104 GLN P 7 GLN P 10 GLN S 61 ASN a 42 HIS j 36 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN m 73 ASN m 122 ASN m 146 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 GLN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 35 GLN y 31 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 152207 Z= 0.414 Angle : 1.096 11.690 229001 Z= 0.530 Chirality : 0.053 0.369 29444 Planarity : 0.009 0.163 11367 Dihedral : 23.945 179.807 79426 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 4.35 % Allowed : 13.52 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 4751 helix: -0.36 (0.12), residues: 1527 sheet: -0.98 (0.16), residues: 907 loop : -1.12 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP v 101 HIS 0.014 0.003 HIS 1 69 PHE 0.034 0.004 PHE D 118 TYR 0.032 0.004 TYR O 36 ARG 0.021 0.002 ARG s 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 785 time to evaluate : 5.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5638 (mttt) cc_final: 0.4976 (mptt) REVERT: C 68 LYS cc_start: 0.6688 (mttt) cc_final: 0.6477 (mttm) REVERT: C 111 LYS cc_start: 0.5048 (ptmm) cc_final: 0.4806 (ptpp) REVERT: C 125 LYS cc_start: 0.5198 (pttt) cc_final: 0.4855 (ptpt) REVERT: C 133 ARG cc_start: 0.5616 (ptt-90) cc_final: 0.5055 (ttm-80) REVERT: C 163 GLN cc_start: 0.6761 (tt0) cc_final: 0.6226 (mt0) REVERT: C 182 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6719 (ttt180) REVERT: C 183 LYS cc_start: 0.6099 (mttt) cc_final: 0.5749 (mtpt) REVERT: C 199 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6001 (pt0) REVERT: C 201 MET cc_start: 0.6967 (ptt) cc_final: 0.6680 (ptm) REVERT: C 269 ARG cc_start: 0.5955 (ttp-170) cc_final: 0.5188 (ttp80) REVERT: D 7 LYS cc_start: 0.6971 (ttpp) cc_final: 0.6756 (ttpt) REVERT: D 17 GLU cc_start: 0.4303 (tt0) cc_final: 0.3944 (mp0) REVERT: D 42 ASN cc_start: 0.5059 (t0) cc_final: 0.4703 (t0) REVERT: D 55 LYS cc_start: 0.5063 (ttmm) cc_final: 0.4741 (ttmt) REVERT: D 70 LYS cc_start: 0.4997 (tttt) cc_final: 0.4699 (tptt) REVERT: D 74 GLU cc_start: 0.4869 (tt0) cc_final: 0.4534 (mp0) REVERT: D 99 GLU cc_start: 0.5160 (tp30) cc_final: 0.4770 (pt0) REVERT: D 105 LYS cc_start: 0.5595 (mttt) cc_final: 0.5377 (mmmm) REVERT: D 128 ARG cc_start: 0.7104 (mtt90) cc_final: 0.6286 (mtp180) REVERT: D 131 ASP cc_start: 0.7039 (m-30) cc_final: 0.6607 (m-30) REVERT: D 183 GLU cc_start: 0.4647 (OUTLIER) cc_final: 0.4442 (tp30) REVERT: E 22 ASP cc_start: 0.3909 (t0) cc_final: 0.3494 (p0) REVERT: E 57 LYS cc_start: 0.6382 (tttp) cc_final: 0.6151 (tptm) REVERT: E 61 ARG cc_start: 0.6824 (ptm160) cc_final: 0.6301 (ptt-90) REVERT: E 106 LYS cc_start: 0.5691 (mtmt) cc_final: 0.5251 (mttt) REVERT: E 120 VAL cc_start: 0.4994 (t) cc_final: 0.4693 (p) REVERT: E 167 VAL cc_start: 0.5671 (t) cc_final: 0.5103 (m) REVERT: E 188 MET cc_start: 0.5153 (mtp) cc_final: 0.4889 (mtt) REVERT: E 199 MET cc_start: 0.4307 (ttp) cc_final: 0.4098 (ttm) REVERT: F 83 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.3738 (m-80) REVERT: F 89 VAL cc_start: 0.6329 (OUTLIER) cc_final: 0.5901 (m) REVERT: F 94 GLU cc_start: 0.4385 (mp0) cc_final: 0.4033 (tt0) REVERT: F 125 ARG cc_start: 0.3816 (mmt90) cc_final: 0.3576 (mmt90) REVERT: F 130 MET cc_start: 0.5579 (ptm) cc_final: 0.5083 (ppp) REVERT: F 133 ARG cc_start: 0.4182 (mtt-85) cc_final: 0.3911 (mtp85) REVERT: G 85 LYS cc_start: 0.4399 (OUTLIER) cc_final: 0.4143 (tppt) REVERT: G 88 GLN cc_start: 0.5109 (pt0) cc_final: 0.4786 (pt0) REVERT: G 99 LYS cc_start: 0.4152 (mtmm) cc_final: 0.3909 (tptm) REVERT: G 143 GLN cc_start: 0.6350 (tp40) cc_final: 0.6033 (tp40) REVERT: G 152 ARG cc_start: 0.6010 (tpp-160) cc_final: 0.5161 (mmt180) REVERT: H 22 LYS cc_start: 0.5713 (mmtp) cc_final: 0.5268 (mttp) REVERT: J 19 ASP cc_start: 0.6409 (t0) cc_final: 0.6207 (t0) REVERT: J 61 LYS cc_start: 0.6359 (mtmm) cc_final: 0.5583 (mmtm) REVERT: J 85 LYS cc_start: 0.6516 (mttm) cc_final: 0.5921 (mmtm) REVERT: J 90 GLU cc_start: 0.6207 (pt0) cc_final: 0.5216 (tp30) REVERT: J 95 ARG cc_start: 0.5260 (ttm-80) cc_final: 0.5012 (ttp80) REVERT: J 99 ARG cc_start: 0.5960 (mmm160) cc_final: 0.5500 (mmp-170) REVERT: J 138 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5403 (pt0) REVERT: K 20 MET cc_start: 0.7436 (ttp) cc_final: 0.7178 (ttm) REVERT: K 53 LYS cc_start: 0.5377 (pttp) cc_final: 0.4825 (tptp) REVERT: K 88 ASN cc_start: 0.5808 (t0) cc_final: 0.5373 (t0) REVERT: K 98 ARG cc_start: 0.5870 (mmt180) cc_final: 0.5663 (mmp80) REVERT: K 113 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4210 (tpt) REVERT: K 114 LYS cc_start: 0.5028 (tptt) cc_final: 0.4712 (tttm) REVERT: K 121 GLU cc_start: 0.6362 (tt0) cc_final: 0.5990 (tt0) REVERT: L 14 LYS cc_start: 0.5499 (tttt) cc_final: 0.5236 (ttpt) REVERT: L 103 ILE cc_start: 0.5872 (mt) cc_final: 0.5627 (pp) REVERT: M 5 LYS cc_start: 0.6095 (mtpt) cc_final: 0.5876 (mtpp) REVERT: M 6 ARG cc_start: 0.5402 (ttt-90) cc_final: 0.4899 (mtm-85) REVERT: M 30 SER cc_start: 0.6756 (m) cc_final: 0.6194 (p) REVERT: M 55 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5861 (ttt90) REVERT: M 59 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.5712 (mtm180) REVERT: M 115 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5279 (tt0) REVERT: M 118 LYS cc_start: 0.5831 (mmtm) cc_final: 0.5540 (ttmp) REVERT: M 133 LYS cc_start: 0.5393 (ttpp) cc_final: 0.5092 (tttm) REVERT: M 136 MET cc_start: 0.3356 (mtp) cc_final: 0.3121 (mtt) REVERT: N 117 ASP cc_start: 0.4513 (OUTLIER) cc_final: 0.4192 (t0) REVERT: O 17 LYS cc_start: 0.5102 (mmtp) cc_final: 0.4848 (tppt) REVERT: O 19 GLN cc_start: 0.5563 (tm-30) cc_final: 0.5353 (tm-30) REVERT: O 31 THR cc_start: 0.6107 (m) cc_final: 0.5862 (p) REVERT: O 91 SER cc_start: 0.6141 (m) cc_final: 0.5558 (p) REVERT: P 6 LYS cc_start: 0.5307 (tptt) cc_final: 0.5054 (mtmt) REVERT: P 7 GLN cc_start: 0.5765 (tt0) cc_final: 0.5031 (mm-40) REVERT: P 13 MET cc_start: 0.5636 (mtp) cc_final: 0.5332 (mmm) REVERT: P 33 VAL cc_start: 0.4764 (t) cc_final: 0.4320 (p) REVERT: P 89 ARG cc_start: 0.5588 (mtm-85) cc_final: 0.4919 (mtt-85) REVERT: P 111 LYS cc_start: 0.5819 (mmmt) cc_final: 0.5617 (mttm) REVERT: Q 11 ARG cc_start: 0.6146 (tpm170) cc_final: 0.5468 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6330 (mtpp) cc_final: 0.6022 (mtmp) REVERT: Q 84 LYS cc_start: 0.5582 (ttpp) cc_final: 0.4969 (mmtm) REVERT: Q 87 SER cc_start: 0.5763 (OUTLIER) cc_final: 0.5450 (m) REVERT: Q 89 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4821 (mm-30) REVERT: Q 103 LYS cc_start: 0.5340 (mmtt) cc_final: 0.4402 (mmmt) REVERT: R 6 GLN cc_start: 0.5793 (tt0) cc_final: 0.5310 (pt0) REVERT: R 13 ARG cc_start: 0.6461 (ttp80) cc_final: 0.5834 (ttp-170) REVERT: R 34 GLU cc_start: 0.5055 (mt-10) cc_final: 0.4684 (mp0) REVERT: R 60 LYS cc_start: 0.4709 (mttp) cc_final: 0.4422 (mtpt) REVERT: R 86 GLN cc_start: 0.6601 (pt0) cc_final: 0.6074 (mt0) REVERT: S 11 ARG cc_start: 0.5822 (mmt-90) cc_final: 0.5380 (mmm-85) REVERT: S 12 SER cc_start: 0.6837 (t) cc_final: 0.6520 (p) REVERT: S 59 GLU cc_start: 0.4816 (mt-10) cc_final: 0.4595 (mm-30) REVERT: T 4 GLU cc_start: 0.5015 (tt0) cc_final: 0.4787 (tt0) REVERT: T 5 GLU cc_start: 0.4621 (mp0) cc_final: 0.4409 (tt0) REVERT: T 8 LEU cc_start: 0.6143 (mt) cc_final: 0.5855 (mt) REVERT: T 33 LYS cc_start: 0.6053 (ttmt) cc_final: 0.5848 (mtpp) REVERT: T 56 GLU cc_start: 0.5404 (tp30) cc_final: 0.5022 (tp30) REVERT: T 69 ARG cc_start: 0.4621 (ptt-90) cc_final: 0.4289 (mtp85) REVERT: T 73 ARG cc_start: 0.3236 (tpt170) cc_final: 0.2880 (ttp-110) REVERT: U 9 ASP cc_start: 0.4914 (m-30) cc_final: 0.4093 (m-30) REVERT: U 26 LYS cc_start: 0.4883 (mmmt) cc_final: 0.4432 (mttm) REVERT: U 31 SER cc_start: 0.4977 (p) cc_final: 0.4752 (p) REVERT: U 46 GLN cc_start: 0.5134 (pt0) cc_final: 0.4860 (mt0) REVERT: V 11 GLU cc_start: 0.5023 (pt0) cc_final: 0.4515 (mt-10) REVERT: V 43 ASP cc_start: 0.5979 (t0) cc_final: 0.5325 (m-30) REVERT: V 48 MET cc_start: 0.5411 (tpt) cc_final: 0.4915 (tpt) REVERT: V 82 TYR cc_start: 0.6082 (p90) cc_final: 0.5774 (p90) REVERT: W 29 GLU cc_start: 0.6787 (tt0) cc_final: 0.6381 (mt-10) REVERT: W 39 ARG cc_start: 0.6509 (mtt-85) cc_final: 0.5959 (mtm180) REVERT: W 44 LYS cc_start: 0.6673 (tttt) cc_final: 0.6277 (mtpt) REVERT: W 72 LYS cc_start: 0.5601 (mmmt) cc_final: 0.5116 (mmtm) REVERT: W 78 LYS cc_start: 0.6276 (mttt) cc_final: 0.5729 (mtmm) REVERT: Y 14 LEU cc_start: 0.4918 (mt) cc_final: 0.4668 (mp) REVERT: Y 29 ARG cc_start: 0.5135 (mtm-85) cc_final: 0.4649 (ttm-80) REVERT: Z 56 LYS cc_start: 0.5785 (tmtt) cc_final: 0.5416 (ttmt) REVERT: a 37 LYS cc_start: 0.6111 (mtmm) cc_final: 0.5676 (mttp) REVERT: a 52 ARG cc_start: 0.4840 (ptp90) cc_final: 0.4350 (ttt180) REVERT: b 7 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5489 (tt0) REVERT: b 10 LYS cc_start: 0.5203 (mptt) cc_final: 0.4473 (mtpt) REVERT: b 33 LYS cc_start: 0.5078 (mmtt) cc_final: 0.4757 (mmmm) REVERT: b 35 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5515 (tt0) REVERT: b 44 ARG cc_start: 0.5765 (mtp180) cc_final: 0.4446 (mtp85) REVERT: b 45 GLN cc_start: 0.6163 (tp40) cc_final: 0.5942 (mm110) REVERT: c 12 ARG cc_start: 0.6914 (ttp80) cc_final: 0.6417 (ttt90) REVERT: c 25 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6059 (tmmt) REVERT: d 16 LYS cc_start: 0.6265 (tptm) cc_final: 0.5806 (tptt) REVERT: j 21 ARG cc_start: 0.3226 (OUTLIER) cc_final: 0.2563 (pmm-80) REVERT: j 49 MET cc_start: 0.3562 (mtm) cc_final: 0.3141 (mtm) REVERT: j 50 PHE cc_start: 0.3220 (OUTLIER) cc_final: 0.2794 (p90) REVERT: j 64 LYS cc_start: 0.3078 (mtpp) cc_final: 0.2720 (ptpp) REVERT: j 105 LYS cc_start: 0.5115 (tttt) cc_final: 0.4681 (tptp) REVERT: j 143 LYS cc_start: 0.3283 (tttp) cc_final: 0.3039 (tptp) REVERT: j 169 GLU cc_start: 0.5590 (mm-30) cc_final: 0.5317 (mm-30) REVERT: m 26 LYS cc_start: 0.4919 (tptp) cc_final: 0.4698 (ttpt) REVERT: m 30 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.6109 (mm) REVERT: m 43 ASN cc_start: 0.4867 (t0) cc_final: 0.4536 (m-40) REVERT: m 45 ARG cc_start: 0.4676 (mmm-85) cc_final: 0.4034 (mmm-85) REVERT: m 55 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3860 (pt0) REVERT: m 61 GLN cc_start: 0.5575 (tt0) cc_final: 0.5193 (tp40) REVERT: m 62 LYS cc_start: 0.5566 (mttt) cc_final: 0.5335 (mttt) REVERT: m 65 GLU cc_start: 0.5432 (tt0) cc_final: 0.5037 (tp30) REVERT: m 73 ASN cc_start: 0.4931 (m110) cc_final: 0.4523 (m-40) REVERT: m 93 ARG cc_start: 0.5566 (mpp-170) cc_final: 0.5311 (mtt90) REVERT: m 142 ASP cc_start: 0.4137 (m-30) cc_final: 0.3831 (t0) REVERT: m 156 LYS cc_start: 0.4091 (mtmm) cc_final: 0.3727 (mtmm) REVERT: n 52 ASN cc_start: 0.3635 (OUTLIER) cc_final: 0.3432 (m-40) REVERT: o 36 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.5095 (ttmp) REVERT: o 40 GLU cc_start: 0.4477 (mt-10) cc_final: 0.4165 (mt-10) REVERT: o 74 GLU cc_start: 0.4757 (pt0) cc_final: 0.4188 (tt0) REVERT: o 76 LYS cc_start: 0.3314 (mmmt) cc_final: 0.3075 (mmtt) REVERT: o 96 ARG cc_start: 0.4331 (ttm-80) cc_final: 0.4086 (ttm170) REVERT: o 106 GLU cc_start: 0.4882 (tt0) cc_final: 0.4314 (mm-30) REVERT: o 123 GLU cc_start: 0.4397 (tp30) cc_final: 0.3810 (tm-30) REVERT: o 144 MET cc_start: 0.4705 (mmm) cc_final: 0.4431 (mtp) REVERT: o 146 GLU cc_start: 0.4309 (mm-30) cc_final: 0.3898 (tm-30) REVERT: p 40 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5199 (mp) REVERT: p 88 ARG cc_start: 0.4021 (mtm180) cc_final: 0.3796 (mtm110) REVERT: p 114 ARG cc_start: 0.3883 (ttm170) cc_final: 0.3652 (ttp80) REVERT: q 65 ILE cc_start: 0.4114 (mt) cc_final: 0.3861 (mp) REVERT: q 85 ARG cc_start: 0.3884 (OUTLIER) cc_final: 0.2440 (mpt-90) REVERT: q 106 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.4088 (tpt90) REVERT: q 119 ARG cc_start: 0.4893 (mtm110) cc_final: 0.4356 (mtt180) REVERT: q 124 ARG cc_start: 0.6029 (ttm-80) cc_final: 0.5623 (mtp180) REVERT: s 52 PHE cc_start: 0.5378 (m-80) cc_final: 0.4988 (m-80) REVERT: t 10 LYS cc_start: 0.4539 (ttpt) cc_final: 0.4250 (tttp) REVERT: t 31 ARG cc_start: 0.4092 (OUTLIER) cc_final: 0.3867 (tmm160) REVERT: t 54 ARG cc_start: 0.4001 (ttp-110) cc_final: 0.3527 (mtp180) REVERT: t 75 GLN cc_start: 0.2034 (OUTLIER) cc_final: 0.1757 (pt0) REVERT: t 86 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.4285 (ttp-110) REVERT: t 95 TYR cc_start: 0.5184 (m-80) cc_final: 0.4800 (m-80) REVERT: t 116 LYS cc_start: 0.4407 (mtpt) cc_final: 0.4061 (mttt) REVERT: u 29 ARG cc_start: 0.4268 (tmt170) cc_final: 0.3730 (tpp-160) REVERT: u 62 LYS cc_start: 0.3091 (mttt) cc_final: 0.2800 (mtpm) REVERT: u 70 ARG cc_start: 0.4154 (mtt-85) cc_final: 0.3931 (mtm-85) REVERT: u 72 GLU cc_start: 0.4388 (mt-10) cc_final: 0.3564 (tp30) REVERT: u 81 MET cc_start: 0.4821 (mtt) cc_final: 0.4251 (mmm) REVERT: u 93 ARG cc_start: 0.4306 (mtp85) cc_final: 0.4065 (mmt90) REVERT: v 21 PHE cc_start: 0.1736 (OUTLIER) cc_final: 0.1254 (m-80) REVERT: v 47 LYS cc_start: 0.3261 (mmtm) cc_final: 0.2569 (ptpt) REVERT: v 89 MET cc_start: 0.5853 (mmt) cc_final: 0.5626 (mmp) REVERT: v 90 ARG cc_start: 0.5839 (mtt90) cc_final: 0.4919 (mtt90) REVERT: v 98 LYS cc_start: 0.5001 (mmmt) cc_final: 0.4181 (mmmm) REVERT: w 38 HIS cc_start: 0.5179 (t70) cc_final: 0.4644 (t-90) REVERT: w 58 ARG cc_start: 0.5887 (ttt-90) cc_final: 0.5610 (ttp80) REVERT: w 59 MET cc_start: 0.6844 (mtt) cc_final: 0.6456 (mtp) REVERT: w 71 LYS cc_start: 0.5240 (tttt) cc_final: 0.4791 (tttm) REVERT: w 73 LYS cc_start: 0.3315 (mmmt) cc_final: 0.3054 (mmtp) REVERT: w 84 ARG cc_start: 0.3426 (ttt180) cc_final: 0.3186 (tmt90) REVERT: y 37 PHE cc_start: 0.6013 (m-80) cc_final: 0.5646 (m-80) REVERT: z 61 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5121 (mtp180) REVERT: 1 49 ILE cc_start: 0.3941 (OUTLIER) cc_final: 0.3569 (mp) REVERT: 1 63 THR cc_start: 0.3434 (OUTLIER) cc_final: 0.3201 (t) REVERT: 1 66 MET cc_start: 0.4571 (mtt) cc_final: 0.3862 (mtt) REVERT: 2 10 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.3843 (mmm160) REVERT: 3 21 ARG cc_start: 0.3516 (mmt-90) cc_final: 0.3249 (mmm160) REVERT: 3 32 VAL cc_start: 0.5230 (t) cc_final: 0.4807 (m) REVERT: 3 36 GLU cc_start: 0.6490 (tt0) cc_final: 0.6136 (mt-10) REVERT: 3 39 GLU cc_start: 0.5949 (tm-30) cc_final: 0.5268 (pp20) REVERT: 3 40 LYS cc_start: 0.5939 (tptt) cc_final: 0.5293 (tttp) REVERT: 3 45 ARG cc_start: 0.4667 (OUTLIER) cc_final: 0.4442 (mmt180) REVERT: 3 46 LYS cc_start: 0.4799 (ttmt) cc_final: 0.4540 (ttpt) REVERT: e 8 LYS cc_start: 0.6157 (mtpt) cc_final: 0.5762 (ptpt) REVERT: e 15 LYS cc_start: 0.6276 (tttm) cc_final: 0.5610 (tptt) REVERT: e 30 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4803 (mm-30) outliers start: 172 outliers final: 88 residues processed: 899 average time/residue: 2.4016 time to fit residues: 3013.2499 Evaluate side-chains 864 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 746 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain U residue 24 LYS Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 45 LYS Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 159 ASP Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 71 MET Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 86 ARG Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 49 ILE Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 70 LYS Chi-restraints excluded: chain 2 residue 10 ARG Chi-restraints excluded: chain 2 residue 18 ARG Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 840 optimal weight: 4.9990 chunk 639 optimal weight: 30.0000 chunk 441 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 405 optimal weight: 20.0000 chunk 571 optimal weight: 8.9990 chunk 853 optimal weight: 2.9990 chunk 903 optimal weight: 8.9990 chunk 446 optimal weight: 0.9980 chunk 809 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 63 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN O 38 GLN O 104 GLN S 61 ASN j 39 HIS j 170 HIS j 177 ASN m 122 ASN s 64 GLN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 152207 Z= 0.177 Angle : 0.663 8.428 229001 Z= 0.345 Chirality : 0.038 0.297 29444 Planarity : 0.005 0.068 11367 Dihedral : 23.695 179.641 79426 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 15.41 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 4751 helix: 0.43 (0.13), residues: 1533 sheet: -0.80 (0.16), residues: 931 loop : -0.85 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.008 0.002 HIS V 44 PHE 0.020 0.002 PHE U 95 TYR 0.021 0.002 TYR S 38 ARG 0.008 0.001 ARG s 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 749 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5614 (mttt) cc_final: 0.5008 (mptt) REVERT: C 111 LYS cc_start: 0.5048 (ptmm) cc_final: 0.4805 (ptpp) REVERT: C 125 LYS cc_start: 0.5172 (pttt) cc_final: 0.4868 (ptpt) REVERT: C 133 ARG cc_start: 0.5727 (ptt-90) cc_final: 0.5071 (ttm-80) REVERT: C 163 GLN cc_start: 0.6661 (tt0) cc_final: 0.6100 (mt0) REVERT: C 182 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6684 (ttt180) REVERT: C 183 LYS cc_start: 0.5943 (mttt) cc_final: 0.5596 (mtpt) REVERT: C 199 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6010 (pt0) REVERT: C 201 MET cc_start: 0.7006 (ptt) cc_final: 0.6724 (ptm) REVERT: C 269 ARG cc_start: 0.6020 (ttp-170) cc_final: 0.5272 (ttp80) REVERT: D 7 LYS cc_start: 0.6972 (ttpp) cc_final: 0.6697 (ttpp) REVERT: D 17 GLU cc_start: 0.4196 (tt0) cc_final: 0.3906 (mp0) REVERT: D 42 ASN cc_start: 0.5279 (t0) cc_final: 0.4991 (t0) REVERT: D 55 LYS cc_start: 0.5103 (ttmm) cc_final: 0.4766 (ttmt) REVERT: D 70 LYS cc_start: 0.5076 (tttt) cc_final: 0.4720 (tptt) REVERT: D 74 GLU cc_start: 0.4871 (tt0) cc_final: 0.4557 (mp0) REVERT: D 99 GLU cc_start: 0.5340 (tp30) cc_final: 0.4893 (pt0) REVERT: D 105 LYS cc_start: 0.5814 (mttt) cc_final: 0.5436 (mmmt) REVERT: D 128 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6330 (mtp180) REVERT: D 131 ASP cc_start: 0.6938 (m-30) cc_final: 0.6484 (m-30) REVERT: E 22 ASP cc_start: 0.3966 (t0) cc_final: 0.3442 (p0) REVERT: E 61 ARG cc_start: 0.6869 (ptm160) cc_final: 0.6325 (ptt-90) REVERT: E 106 LYS cc_start: 0.5750 (mtmt) cc_final: 0.5340 (mttt) REVERT: E 170 ARG cc_start: 0.4998 (tpp-160) cc_final: 0.4539 (tpp80) REVERT: E 199 MET cc_start: 0.4340 (ttp) cc_final: 0.4102 (ttm) REVERT: F 94 GLU cc_start: 0.4577 (mp0) cc_final: 0.4335 (tt0) REVERT: F 125 ARG cc_start: 0.3833 (mmt90) cc_final: 0.3608 (mmt90) REVERT: F 133 ARG cc_start: 0.4214 (mtt-85) cc_final: 0.3703 (mtp85) REVERT: G 71 LEU cc_start: 0.5140 (mt) cc_final: 0.4674 (mp) REVERT: G 73 ASN cc_start: 0.5579 (t0) cc_final: 0.5181 (t0) REVERT: G 88 GLN cc_start: 0.5208 (pt0) cc_final: 0.4158 (tp40) REVERT: G 99 LYS cc_start: 0.4349 (mtmm) cc_final: 0.3927 (tptt) REVERT: G 143 GLN cc_start: 0.6318 (tp40) cc_final: 0.5984 (tp40) REVERT: H 1 MET cc_start: 0.3503 (tmm) cc_final: 0.2495 (mmp) REVERT: H 19 VAL cc_start: 0.3891 (t) cc_final: 0.3521 (p) REVERT: H 22 LYS cc_start: 0.5775 (mmtp) cc_final: 0.5325 (mttp) REVERT: J 31 GLU cc_start: 0.6319 (tp30) cc_final: 0.6000 (tm-30) REVERT: J 39 LYS cc_start: 0.6538 (mtpp) cc_final: 0.6218 (mmmm) REVERT: J 61 LYS cc_start: 0.6333 (mtmm) cc_final: 0.5587 (mmtm) REVERT: J 85 LYS cc_start: 0.6557 (mttm) cc_final: 0.5919 (mmtm) REVERT: J 90 GLU cc_start: 0.6274 (pt0) cc_final: 0.5337 (tp30) REVERT: J 95 ARG cc_start: 0.5116 (ttm-80) cc_final: 0.4796 (ttp80) REVERT: J 96 ARG cc_start: 0.4615 (ttt180) cc_final: 0.3815 (mmt-90) REVERT: J 99 ARG cc_start: 0.5839 (mmm160) cc_final: 0.5513 (mmp-170) REVERT: J 129 GLU cc_start: 0.5492 (mm-30) cc_final: 0.5155 (tp30) REVERT: J 138 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.5387 (pt0) REVERT: K 20 MET cc_start: 0.7444 (ttp) cc_final: 0.7203 (ttm) REVERT: K 53 LYS cc_start: 0.5528 (pttp) cc_final: 0.4899 (tptp) REVERT: K 88 ASN cc_start: 0.5784 (t0) cc_final: 0.5364 (t0) REVERT: K 98 ARG cc_start: 0.5919 (mmt180) cc_final: 0.5126 (mmm-85) REVERT: K 113 MET cc_start: 0.4428 (OUTLIER) cc_final: 0.4222 (tpt) REVERT: K 114 LYS cc_start: 0.5027 (tptt) cc_final: 0.4708 (tttm) REVERT: K 121 GLU cc_start: 0.6267 (tt0) cc_final: 0.5983 (tt0) REVERT: L 14 LYS cc_start: 0.5494 (tttt) cc_final: 0.5196 (ttpt) REVERT: L 17 LYS cc_start: 0.6671 (mttt) cc_final: 0.6385 (mttm) REVERT: L 103 ILE cc_start: 0.5815 (mt) cc_final: 0.5597 (pp) REVERT: L 123 ARG cc_start: 0.4724 (ttm-80) cc_final: 0.4179 (mtt90) REVERT: M 5 LYS cc_start: 0.6089 (mtpt) cc_final: 0.5871 (mtpp) REVERT: M 6 ARG cc_start: 0.5317 (ttt-90) cc_final: 0.4770 (mtp85) REVERT: M 30 SER cc_start: 0.6894 (m) cc_final: 0.6446 (p) REVERT: M 36 VAL cc_start: 0.6770 (t) cc_final: 0.6537 (m) REVERT: M 55 ARG cc_start: 0.6297 (tpp80) cc_final: 0.5992 (ttt90) REVERT: M 59 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5981 (mtm180) REVERT: M 106 ASP cc_start: 0.6656 (t0) cc_final: 0.6417 (t70) REVERT: M 115 GLU cc_start: 0.5599 (mm-30) cc_final: 0.5243 (tt0) REVERT: M 118 LYS cc_start: 0.5813 (mmtm) cc_final: 0.5564 (ttmp) REVERT: M 127 LYS cc_start: 0.6053 (ttmt) cc_final: 0.5444 (tptp) REVERT: M 136 MET cc_start: 0.3758 (mtp) cc_final: 0.3416 (mtt) REVERT: N 73 ASN cc_start: 0.6279 (m-40) cc_final: 0.5893 (m-40) REVERT: O 16 ARG cc_start: 0.5750 (mmp80) cc_final: 0.5278 (mmt90) REVERT: O 17 LYS cc_start: 0.5178 (mmtp) cc_final: 0.4904 (tppt) REVERT: O 19 GLN cc_start: 0.5633 (tm-30) cc_final: 0.5405 (tm-30) REVERT: O 31 THR cc_start: 0.6268 (m) cc_final: 0.6046 (p) REVERT: O 91 SER cc_start: 0.6143 (m) cc_final: 0.5518 (p) REVERT: P 7 GLN cc_start: 0.5717 (tt0) cc_final: 0.4876 (mm-40) REVERT: P 13 MET cc_start: 0.5669 (mtp) cc_final: 0.5355 (mmm) REVERT: P 33 VAL cc_start: 0.4756 (t) cc_final: 0.4336 (m) REVERT: P 89 ARG cc_start: 0.5668 (mtm-85) cc_final: 0.4979 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6189 (tpm170) cc_final: 0.5452 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6327 (mtpp) cc_final: 0.5966 (mtmp) REVERT: Q 84 LYS cc_start: 0.5518 (ttpp) cc_final: 0.4936 (mmtm) REVERT: Q 87 SER cc_start: 0.5852 (OUTLIER) cc_final: 0.5551 (m) REVERT: Q 89 GLU cc_start: 0.5488 (mt-10) cc_final: 0.4838 (mm-30) REVERT: R 6 GLN cc_start: 0.5616 (tt0) cc_final: 0.5191 (pt0) REVERT: R 13 ARG cc_start: 0.6455 (ttp80) cc_final: 0.5866 (ttp-170) REVERT: R 34 GLU cc_start: 0.5026 (mt-10) cc_final: 0.4601 (mp0) REVERT: R 60 LYS cc_start: 0.4570 (mttp) cc_final: 0.4253 (mtpt) REVERT: R 86 GLN cc_start: 0.6602 (pt0) cc_final: 0.6237 (pm20) REVERT: S 11 ARG cc_start: 0.5780 (mmt-90) cc_final: 0.5313 (mmm-85) REVERT: S 12 SER cc_start: 0.6739 (t) cc_final: 0.6468 (p) REVERT: S 68 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.4858 (p0) REVERT: T 5 GLU cc_start: 0.4553 (mp0) cc_final: 0.4312 (tt0) REVERT: T 8 LEU cc_start: 0.6193 (mt) cc_final: 0.5866 (mt) REVERT: T 36 LYS cc_start: 0.4874 (OUTLIER) cc_final: 0.4649 (tttt) REVERT: T 56 GLU cc_start: 0.5420 (tp30) cc_final: 0.4943 (tp30) REVERT: T 69 ARG cc_start: 0.4641 (ptt-90) cc_final: 0.4359 (ptm-80) REVERT: T 73 ARG cc_start: 0.3287 (tpt170) cc_final: 0.2895 (ttp-110) REVERT: U 9 ASP cc_start: 0.4968 (m-30) cc_final: 0.4288 (m-30) REVERT: U 46 GLN cc_start: 0.4967 (pt0) cc_final: 0.4675 (mt0) REVERT: V 11 GLU cc_start: 0.4960 (pt0) cc_final: 0.4526 (mt-10) REVERT: V 43 ASP cc_start: 0.5815 (t0) cc_final: 0.5196 (m-30) REVERT: V 48 MET cc_start: 0.5322 (tpt) cc_final: 0.4732 (tpt) REVERT: V 82 TYR cc_start: 0.6169 (p90) cc_final: 0.5867 (p90) REVERT: W 29 GLU cc_start: 0.6746 (tt0) cc_final: 0.6225 (mt-10) REVERT: W 39 ARG cc_start: 0.6510 (mtt-85) cc_final: 0.5936 (mtm180) REVERT: W 44 LYS cc_start: 0.6631 (tttt) cc_final: 0.6238 (mtpt) REVERT: W 66 LYS cc_start: 0.6692 (mttt) cc_final: 0.6098 (mtpt) REVERT: W 72 LYS cc_start: 0.5514 (mmmt) cc_final: 0.5138 (mmtt) REVERT: W 78 LYS cc_start: 0.6308 (mttt) cc_final: 0.5794 (mtmm) REVERT: Y 14 LEU cc_start: 0.4698 (mt) cc_final: 0.4452 (mp) REVERT: Y 29 ARG cc_start: 0.5116 (mtm-85) cc_final: 0.4577 (ttm-80) REVERT: Y 46 VAL cc_start: 0.5517 (t) cc_final: 0.5295 (p) REVERT: Z 56 LYS cc_start: 0.5683 (tmtt) cc_final: 0.5319 (ttmt) REVERT: a 37 LYS cc_start: 0.6146 (mtmm) cc_final: 0.5656 (mptp) REVERT: a 52 ARG cc_start: 0.4806 (ptp90) cc_final: 0.4489 (ttp80) REVERT: b 7 GLU cc_start: 0.5804 (mt-10) cc_final: 0.5434 (tt0) REVERT: b 10 LYS cc_start: 0.5067 (mptt) cc_final: 0.4335 (mtpt) REVERT: b 33 LYS cc_start: 0.5054 (mmtt) cc_final: 0.4725 (mmmm) REVERT: b 35 GLU cc_start: 0.5980 (mt-10) cc_final: 0.5564 (tt0) REVERT: b 44 ARG cc_start: 0.5630 (mtp180) cc_final: 0.4330 (mtp85) REVERT: c 12 ARG cc_start: 0.7027 (ttp80) cc_final: 0.6419 (ttt90) REVERT: c 25 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5951 (tmmt) REVERT: d 16 LYS cc_start: 0.6385 (tptm) cc_final: 0.6036 (tptt) REVERT: j 21 ARG cc_start: 0.3094 (OUTLIER) cc_final: 0.2399 (pmm-80) REVERT: j 39 HIS cc_start: 0.5156 (m-70) cc_final: 0.4954 (m90) REVERT: j 47 VAL cc_start: 0.3551 (t) cc_final: 0.3319 (t) REVERT: j 49 MET cc_start: 0.3407 (mtm) cc_final: 0.3030 (mtm) REVERT: j 50 PHE cc_start: 0.2957 (OUTLIER) cc_final: 0.2565 (p90) REVERT: j 105 LYS cc_start: 0.5157 (tttt) cc_final: 0.4699 (tptp) REVERT: j 143 LYS cc_start: 0.3306 (tttp) cc_final: 0.2987 (tptt) REVERT: j 169 GLU cc_start: 0.5717 (mm-30) cc_final: 0.5498 (mm-30) REVERT: j 188 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5667 (t0) REVERT: m 13 GLU cc_start: 0.4904 (pt0) cc_final: 0.4573 (mt-10) REVERT: m 26 LYS cc_start: 0.5041 (tptp) cc_final: 0.4805 (ttpt) REVERT: m 30 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6159 (mm) REVERT: m 43 ASN cc_start: 0.4882 (t0) cc_final: 0.4537 (m-40) REVERT: m 55 GLU cc_start: 0.4556 (mm-30) cc_final: 0.3835 (pt0) REVERT: m 61 GLN cc_start: 0.5685 (tt0) cc_final: 0.5277 (tp40) REVERT: m 62 LYS cc_start: 0.5616 (mttt) cc_final: 0.5363 (mttt) REVERT: m 64 MET cc_start: 0.5385 (mmt) cc_final: 0.5033 (mmt) REVERT: m 65 GLU cc_start: 0.5537 (tt0) cc_final: 0.5176 (tp30) REVERT: m 73 ASN cc_start: 0.5153 (m110) cc_final: 0.4743 (m-40) REVERT: m 93 ARG cc_start: 0.5477 (mpp-170) cc_final: 0.5236 (mtt90) REVERT: m 142 ASP cc_start: 0.4056 (m-30) cc_final: 0.3806 (t0) REVERT: m 156 LYS cc_start: 0.4145 (mtmm) cc_final: 0.3863 (mtmm) REVERT: n 79 ARG cc_start: 0.3750 (ttm-80) cc_final: 0.3498 (ttm170) REVERT: o 74 GLU cc_start: 0.4773 (pt0) cc_final: 0.4162 (tt0) REVERT: o 76 LYS cc_start: 0.3230 (mmmt) cc_final: 0.3016 (mmtt) REVERT: o 106 GLU cc_start: 0.4817 (tt0) cc_final: 0.4235 (mm-30) REVERT: o 123 GLU cc_start: 0.4383 (tp30) cc_final: 0.3798 (tm-30) REVERT: o 144 MET cc_start: 0.4832 (mmm) cc_final: 0.4584 (mtp) REVERT: o 146 GLU cc_start: 0.4329 (mm-30) cc_final: 0.3903 (tm-30) REVERT: p 29 SER cc_start: 0.5753 (t) cc_final: 0.5313 (m) REVERT: p 40 LEU cc_start: 0.5281 (mt) cc_final: 0.5042 (mp) REVERT: p 69 LYS cc_start: 0.3982 (OUTLIER) cc_final: 0.3651 (tppt) REVERT: q 65 ILE cc_start: 0.4394 (mt) cc_final: 0.4127 (mp) REVERT: q 85 ARG cc_start: 0.4177 (OUTLIER) cc_final: 0.2484 (mpt-90) REVERT: q 119 ARG cc_start: 0.4835 (mtm110) cc_final: 0.4259 (mtt180) REVERT: q 124 ARG cc_start: 0.6031 (ttm-80) cc_final: 0.5474 (mtp180) REVERT: s 52 PHE cc_start: 0.5423 (m-80) cc_final: 0.5107 (m-80) REVERT: s 69 ARG cc_start: 0.4348 (mtm180) cc_final: 0.3817 (mtt180) REVERT: s 82 LEU cc_start: 0.4620 (pt) cc_final: 0.4418 (mt) REVERT: t 29 GLN cc_start: 0.4712 (mp10) cc_final: 0.3544 (mt0) REVERT: t 31 ARG cc_start: 0.4002 (OUTLIER) cc_final: 0.3732 (tmm160) REVERT: t 54 ARG cc_start: 0.3973 (ttp-110) cc_final: 0.3561 (tpp-160) REVERT: t 95 TYR cc_start: 0.5171 (m-80) cc_final: 0.4790 (m-80) REVERT: u 62 LYS cc_start: 0.3267 (mttt) cc_final: 0.2909 (mtpm) REVERT: u 70 ARG cc_start: 0.4230 (mtt-85) cc_final: 0.3926 (mtm-85) REVERT: u 72 GLU cc_start: 0.4314 (mt-10) cc_final: 0.3645 (tp30) REVERT: u 81 MET cc_start: 0.4713 (mtt) cc_final: 0.4288 (mmm) REVERT: u 93 ARG cc_start: 0.4475 (mtp85) cc_final: 0.4227 (mmt90) REVERT: v 21 PHE cc_start: 0.1924 (OUTLIER) cc_final: 0.1470 (m-80) REVERT: v 24 ARG cc_start: 0.3322 (OUTLIER) cc_final: 0.2713 (tpm170) REVERT: v 47 LYS cc_start: 0.3350 (mmtm) cc_final: 0.2684 (ptmm) REVERT: v 89 MET cc_start: 0.5991 (mmt) cc_final: 0.5605 (mmp) REVERT: v 90 ARG cc_start: 0.5876 (mtt90) cc_final: 0.4946 (mtt90) REVERT: v 98 LYS cc_start: 0.5034 (mmmt) cc_final: 0.4334 (mmmm) REVERT: w 38 HIS cc_start: 0.5257 (t70) cc_final: 0.4747 (t-90) REVERT: w 58 ARG cc_start: 0.5796 (ttt-90) cc_final: 0.5570 (ttp80) REVERT: y 4 LYS cc_start: 0.0844 (OUTLIER) cc_final: 0.0382 (tptt) REVERT: y 37 PHE cc_start: 0.6014 (m-80) cc_final: 0.5652 (m-80) REVERT: 1 49 ILE cc_start: 0.3910 (OUTLIER) cc_final: 0.3621 (tt) REVERT: 1 63 THR cc_start: 0.3293 (OUTLIER) cc_final: 0.2973 (t) REVERT: 1 66 MET cc_start: 0.4527 (mtt) cc_final: 0.3878 (mtt) REVERT: 2 16 LYS cc_start: 0.3512 (OUTLIER) cc_final: 0.3145 (mttt) REVERT: 3 21 ARG cc_start: 0.3609 (mmt-90) cc_final: 0.3320 (mmm160) REVERT: 3 32 VAL cc_start: 0.5152 (t) cc_final: 0.4632 (m) REVERT: 3 36 GLU cc_start: 0.6536 (tt0) cc_final: 0.6174 (mt-10) REVERT: 3 39 GLU cc_start: 0.5709 (tm-30) cc_final: 0.5031 (pp20) REVERT: 3 40 LYS cc_start: 0.5834 (tptt) cc_final: 0.5585 (tptm) REVERT: 3 46 LYS cc_start: 0.4859 (ttmt) cc_final: 0.4607 (ttmt) REVERT: e 8 LYS cc_start: 0.6068 (mtpt) cc_final: 0.5545 (ptpt) REVERT: e 15 LYS cc_start: 0.6201 (tttm) cc_final: 0.5558 (tptt) REVERT: e 30 GLU cc_start: 0.5098 (tp30) cc_final: 0.4873 (mm-30) outliers start: 131 outliers final: 64 residues processed: 831 average time/residue: 2.3663 time to fit residues: 2753.1074 Evaluate side-chains 789 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 704 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 17 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 49 ILE Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 752 optimal weight: 8.9990 chunk 513 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 672 optimal weight: 20.0000 chunk 372 optimal weight: 0.2980 chunk 771 optimal weight: 2.9990 chunk 624 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 461 optimal weight: 6.9990 chunk 811 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 ASN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN O 38 GLN O 104 GLN S 61 ASN V 75 GLN b 45 GLN m 122 ASN m 146 ASN s 64 GLN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 GLN v 43 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 152207 Z= 0.190 Angle : 0.681 8.703 229001 Z= 0.351 Chirality : 0.038 0.319 29444 Planarity : 0.005 0.078 11367 Dihedral : 23.658 179.303 79419 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 3.72 % Allowed : 16.15 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4751 helix: 0.52 (0.13), residues: 1546 sheet: -0.71 (0.16), residues: 926 loop : -0.82 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 248 HIS 0.007 0.002 HIS V 44 PHE 0.021 0.002 PHE j 50 TYR 0.022 0.002 TYR j 213 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 720 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5555 (mttt) cc_final: 0.4981 (mptt) REVERT: C 111 LYS cc_start: 0.5258 (ptmm) cc_final: 0.4997 (ptpp) REVERT: C 125 LYS cc_start: 0.5204 (pttt) cc_final: 0.4880 (ptpt) REVERT: C 133 ARG cc_start: 0.5765 (ptt-90) cc_final: 0.5134 (ttm-80) REVERT: C 163 GLN cc_start: 0.6680 (tt0) cc_final: 0.6069 (mt0) REVERT: C 182 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6687 (ttt180) REVERT: C 183 LYS cc_start: 0.6038 (mttt) cc_final: 0.5615 (mmmt) REVERT: C 199 GLU cc_start: 0.6585 (mt-10) cc_final: 0.5981 (pt0) REVERT: C 201 MET cc_start: 0.7015 (ptt) cc_final: 0.6728 (ptm) REVERT: C 214 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6912 (mtt-85) REVERT: C 269 ARG cc_start: 0.6045 (ttp-170) cc_final: 0.5309 (ttt-90) REVERT: D 7 LYS cc_start: 0.6959 (ttpp) cc_final: 0.6685 (ttpp) REVERT: D 17 GLU cc_start: 0.4145 (tt0) cc_final: 0.3892 (mp0) REVERT: D 42 ASN cc_start: 0.5192 (t0) cc_final: 0.4908 (t0) REVERT: D 55 LYS cc_start: 0.5097 (ttmm) cc_final: 0.4754 (ttmt) REVERT: D 70 LYS cc_start: 0.5059 (tttt) cc_final: 0.4756 (tptt) REVERT: D 99 GLU cc_start: 0.5351 (tp30) cc_final: 0.4731 (mp0) REVERT: D 105 LYS cc_start: 0.5954 (mttt) cc_final: 0.5588 (mmmt) REVERT: D 128 ARG cc_start: 0.7114 (mtt90) cc_final: 0.6335 (mtp180) REVERT: D 131 ASP cc_start: 0.6937 (m-30) cc_final: 0.6485 (m-30) REVERT: E 22 ASP cc_start: 0.3920 (t0) cc_final: 0.3475 (p0) REVERT: E 61 ARG cc_start: 0.6902 (ptm160) cc_final: 0.6360 (ptt-90) REVERT: E 170 ARG cc_start: 0.4983 (tpp-160) cc_final: 0.4577 (tpp80) REVERT: E 199 MET cc_start: 0.4367 (ttp) cc_final: 0.4132 (ttm) REVERT: F 38 MET cc_start: 0.5586 (mtm) cc_final: 0.5317 (mtp) REVERT: F 94 GLU cc_start: 0.4539 (mp0) cc_final: 0.4293 (tp30) REVERT: F 125 ARG cc_start: 0.3919 (mmt90) cc_final: 0.3677 (mmt90) REVERT: F 133 ARG cc_start: 0.4414 (mtt-85) cc_final: 0.3857 (mtp85) REVERT: F 150 ARG cc_start: 0.3829 (mtm-85) cc_final: 0.3599 (mtt180) REVERT: F 165 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.4691 (mt-10) REVERT: G 71 LEU cc_start: 0.5241 (mt) cc_final: 0.4766 (mp) REVERT: G 72 LEU cc_start: 0.4664 (mp) cc_final: 0.4302 (mp) REVERT: G 85 LYS cc_start: 0.4344 (tppt) cc_final: 0.4038 (tppt) REVERT: G 99 LYS cc_start: 0.4452 (mtmm) cc_final: 0.4127 (tptt) REVERT: G 143 GLN cc_start: 0.6297 (tp40) cc_final: 0.5953 (tp40) REVERT: G 153 ARG cc_start: 0.4783 (mtt90) cc_final: 0.4469 (ptm-80) REVERT: H 22 LYS cc_start: 0.5827 (mmtp) cc_final: 0.5443 (mttp) REVERT: J 31 GLU cc_start: 0.6314 (tp30) cc_final: 0.6003 (tm-30) REVERT: J 39 LYS cc_start: 0.6547 (mtpp) cc_final: 0.6239 (mmmm) REVERT: J 61 LYS cc_start: 0.6324 (mtmm) cc_final: 0.5583 (mmtm) REVERT: J 85 LYS cc_start: 0.6474 (mttm) cc_final: 0.5890 (mmtm) REVERT: J 90 GLU cc_start: 0.6222 (pt0) cc_final: 0.5296 (tp30) REVERT: J 95 ARG cc_start: 0.5174 (ttm-80) cc_final: 0.4922 (ttp80) REVERT: J 96 ARG cc_start: 0.4600 (ttt180) cc_final: 0.3802 (mmt-90) REVERT: J 99 ARG cc_start: 0.5864 (mmm160) cc_final: 0.5525 (mmp-170) REVERT: J 129 GLU cc_start: 0.5519 (mm-30) cc_final: 0.5175 (tp30) REVERT: J 138 GLN cc_start: 0.5903 (OUTLIER) cc_final: 0.5569 (mp10) REVERT: K 20 MET cc_start: 0.7426 (ttp) cc_final: 0.7174 (ttm) REVERT: K 53 LYS cc_start: 0.5545 (pttp) cc_final: 0.4919 (tptp) REVERT: K 88 ASN cc_start: 0.5729 (t0) cc_final: 0.5287 (t0) REVERT: K 98 ARG cc_start: 0.5916 (mmt180) cc_final: 0.5155 (mtp180) REVERT: K 113 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.4283 (tpt) REVERT: K 114 LYS cc_start: 0.5058 (tptt) cc_final: 0.4736 (tttm) REVERT: K 121 GLU cc_start: 0.6343 (tt0) cc_final: 0.6055 (tt0) REVERT: L 14 LYS cc_start: 0.5484 (tttt) cc_final: 0.5194 (ttpt) REVERT: L 17 LYS cc_start: 0.6610 (mttt) cc_final: 0.6261 (mttm) REVERT: L 103 ILE cc_start: 0.5815 (mt) cc_final: 0.5602 (pp) REVERT: M 5 LYS cc_start: 0.6066 (mtpt) cc_final: 0.5827 (mtpp) REVERT: M 6 ARG cc_start: 0.5381 (ttt-90) cc_final: 0.4785 (mtp85) REVERT: M 30 SER cc_start: 0.6889 (m) cc_final: 0.6478 (p) REVERT: M 36 VAL cc_start: 0.6767 (t) cc_final: 0.6537 (m) REVERT: M 55 ARG cc_start: 0.6220 (tpp-160) cc_final: 0.5885 (ttt90) REVERT: M 59 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5720 (mtm180) REVERT: M 106 ASP cc_start: 0.6595 (t0) cc_final: 0.6347 (t70) REVERT: M 115 GLU cc_start: 0.5553 (mm-30) cc_final: 0.5200 (tt0) REVERT: M 118 LYS cc_start: 0.5820 (mmtm) cc_final: 0.5561 (ttmp) REVERT: M 127 LYS cc_start: 0.6052 (ttmt) cc_final: 0.5437 (tptp) REVERT: M 136 MET cc_start: 0.3684 (mtp) cc_final: 0.3303 (mtt) REVERT: N 73 ASN cc_start: 0.6340 (m-40) cc_final: 0.5968 (m-40) REVERT: O 16 ARG cc_start: 0.5737 (mmp80) cc_final: 0.5044 (mmt90) REVERT: O 17 LYS cc_start: 0.5181 (mmtp) cc_final: 0.4911 (tppt) REVERT: O 19 GLN cc_start: 0.5609 (tm-30) cc_final: 0.5397 (tm-30) REVERT: O 31 THR cc_start: 0.6236 (m) cc_final: 0.6035 (p) REVERT: O 91 SER cc_start: 0.6112 (m) cc_final: 0.5554 (p) REVERT: P 6 LYS cc_start: 0.5166 (tptt) cc_final: 0.4937 (ttpt) REVERT: P 13 MET cc_start: 0.5608 (mtp) cc_final: 0.5260 (mmm) REVERT: P 33 VAL cc_start: 0.4770 (t) cc_final: 0.4305 (m) REVERT: P 89 ARG cc_start: 0.5668 (mtm-85) cc_final: 0.4996 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6072 (tpm170) cc_final: 0.5344 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6326 (mtpp) cc_final: 0.5969 (mtmp) REVERT: Q 84 LYS cc_start: 0.5528 (ttpp) cc_final: 0.4938 (mmtm) REVERT: Q 87 SER cc_start: 0.5846 (OUTLIER) cc_final: 0.5586 (m) REVERT: Q 89 GLU cc_start: 0.5524 (mt-10) cc_final: 0.4872 (mm-30) REVERT: R 6 GLN cc_start: 0.5596 (tt0) cc_final: 0.5204 (pt0) REVERT: R 13 ARG cc_start: 0.6451 (ttp80) cc_final: 0.5889 (ttp-170) REVERT: R 34 GLU cc_start: 0.5173 (mt-10) cc_final: 0.4729 (mp0) REVERT: R 60 LYS cc_start: 0.4513 (mttp) cc_final: 0.4203 (mtpt) REVERT: R 86 GLN cc_start: 0.6591 (pt0) cc_final: 0.6228 (pm20) REVERT: S 11 ARG cc_start: 0.5793 (mmt-90) cc_final: 0.5244 (mmm-85) REVERT: S 12 SER cc_start: 0.6759 (t) cc_final: 0.6468 (p) REVERT: T 5 GLU cc_start: 0.4625 (mp0) cc_final: 0.4375 (tt0) REVERT: T 8 LEU cc_start: 0.6186 (mt) cc_final: 0.5833 (mt) REVERT: T 56 GLU cc_start: 0.5418 (tp30) cc_final: 0.4944 (tp30) REVERT: T 73 ARG cc_start: 0.3261 (tpt170) cc_final: 0.2902 (ttp-110) REVERT: U 9 ASP cc_start: 0.5092 (m-30) cc_final: 0.4564 (m-30) REVERT: U 26 LYS cc_start: 0.4861 (mmmt) cc_final: 0.4425 (mttm) REVERT: U 46 GLN cc_start: 0.4936 (pt0) cc_final: 0.4625 (mt0) REVERT: V 11 GLU cc_start: 0.4845 (pt0) cc_final: 0.4440 (mt-10) REVERT: V 43 ASP cc_start: 0.5809 (t0) cc_final: 0.5190 (m-30) REVERT: V 48 MET cc_start: 0.5328 (tpt) cc_final: 0.4771 (tpt) REVERT: V 61 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4764 (mt) REVERT: V 82 TYR cc_start: 0.6158 (p90) cc_final: 0.5868 (p90) REVERT: W 29 GLU cc_start: 0.6539 (tt0) cc_final: 0.6133 (mt-10) REVERT: W 39 ARG cc_start: 0.6491 (mtt-85) cc_final: 0.5910 (mtm180) REVERT: W 44 LYS cc_start: 0.6619 (tttt) cc_final: 0.6311 (mtpt) REVERT: W 66 LYS cc_start: 0.6704 (mttt) cc_final: 0.6135 (mtpt) REVERT: W 72 LYS cc_start: 0.5293 (mmmt) cc_final: 0.4916 (mmtm) REVERT: W 78 LYS cc_start: 0.6304 (mttt) cc_final: 0.5819 (mtmm) REVERT: Y 14 LEU cc_start: 0.4793 (mt) cc_final: 0.4559 (mp) REVERT: Y 27 ASN cc_start: 0.5022 (m110) cc_final: 0.4636 (m110) REVERT: Y 29 ARG cc_start: 0.5110 (mtm-85) cc_final: 0.4578 (ttm-80) REVERT: Y 46 VAL cc_start: 0.5501 (t) cc_final: 0.5252 (p) REVERT: Z 56 LYS cc_start: 0.5678 (tmtt) cc_final: 0.5140 (ptmm) REVERT: a 37 LYS cc_start: 0.6059 (mtmm) cc_final: 0.5731 (mmmt) REVERT: a 52 ARG cc_start: 0.4811 (ptp90) cc_final: 0.4486 (ttt-90) REVERT: b 7 GLU cc_start: 0.5767 (mt-10) cc_final: 0.5409 (tt0) REVERT: b 10 LYS cc_start: 0.4914 (mptt) cc_final: 0.4499 (ptpt) REVERT: b 33 LYS cc_start: 0.5020 (mmtt) cc_final: 0.4691 (mmmm) REVERT: b 35 GLU cc_start: 0.5960 (mt-10) cc_final: 0.5563 (tt0) REVERT: b 44 ARG cc_start: 0.5679 (mtp180) cc_final: 0.4338 (mtp85) REVERT: c 12 ARG cc_start: 0.7012 (ttp80) cc_final: 0.6395 (ttt90) REVERT: c 25 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5971 (tmmt) REVERT: d 16 LYS cc_start: 0.6414 (tptm) cc_final: 0.6055 (tptt) REVERT: j 21 ARG cc_start: 0.3150 (OUTLIER) cc_final: 0.2343 (pmm-80) REVERT: j 47 VAL cc_start: 0.3555 (t) cc_final: 0.3327 (t) REVERT: j 49 MET cc_start: 0.3438 (mtm) cc_final: 0.3103 (mtm) REVERT: j 50 PHE cc_start: 0.2906 (OUTLIER) cc_final: 0.2596 (p90) REVERT: j 105 LYS cc_start: 0.5046 (tttt) cc_final: 0.4620 (tptp) REVERT: j 143 LYS cc_start: 0.3095 (tttp) cc_final: 0.2762 (mppt) REVERT: j 169 GLU cc_start: 0.5699 (mm-30) cc_final: 0.5477 (mm-30) REVERT: m 13 GLU cc_start: 0.5011 (pt0) cc_final: 0.4545 (pm20) REVERT: m 26 LYS cc_start: 0.4994 (tptp) cc_final: 0.4757 (ttpt) REVERT: m 30 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6122 (mm) REVERT: m 43 ASN cc_start: 0.4852 (t0) cc_final: 0.4515 (m-40) REVERT: m 45 ARG cc_start: 0.4835 (mmm-85) cc_final: 0.4156 (mmm-85) REVERT: m 55 GLU cc_start: 0.4582 (mm-30) cc_final: 0.3872 (pt0) REVERT: m 61 GLN cc_start: 0.5656 (tt0) cc_final: 0.5174 (tp40) REVERT: m 64 MET cc_start: 0.5376 (mmt) cc_final: 0.5057 (mmt) REVERT: m 65 GLU cc_start: 0.5592 (tt0) cc_final: 0.5190 (tp30) REVERT: m 73 ASN cc_start: 0.5264 (m110) cc_final: 0.4909 (m-40) REVERT: m 93 ARG cc_start: 0.5533 (mpp-170) cc_final: 0.5272 (mtt90) REVERT: m 142 ASP cc_start: 0.4086 (m-30) cc_final: 0.3798 (t0) REVERT: n 79 ARG cc_start: 0.3651 (ttm-80) cc_final: 0.3392 (ttm170) REVERT: o 74 GLU cc_start: 0.4758 (pt0) cc_final: 0.4130 (tt0) REVERT: o 76 LYS cc_start: 0.3207 (mmmt) cc_final: 0.2965 (mptt) REVERT: o 104 ILE cc_start: 0.5791 (OUTLIER) cc_final: 0.5481 (mm) REVERT: o 106 GLU cc_start: 0.4795 (tt0) cc_final: 0.4201 (mm-30) REVERT: o 123 GLU cc_start: 0.4483 (tp30) cc_final: 0.3876 (tm-30) REVERT: o 144 MET cc_start: 0.4994 (mmm) cc_final: 0.4779 (mtp) REVERT: o 146 GLU cc_start: 0.4263 (mm-30) cc_final: 0.3860 (tm-30) REVERT: p 40 LEU cc_start: 0.5238 (mt) cc_final: 0.5009 (mp) REVERT: p 69 LYS cc_start: 0.4015 (OUTLIER) cc_final: 0.3671 (tppt) REVERT: q 65 ILE cc_start: 0.4452 (mt) cc_final: 0.4205 (mp) REVERT: q 85 ARG cc_start: 0.4159 (OUTLIER) cc_final: 0.2404 (mpt-90) REVERT: q 119 ARG cc_start: 0.4855 (mtm110) cc_final: 0.4299 (mtt180) REVERT: q 124 ARG cc_start: 0.5962 (ttm-80) cc_final: 0.5456 (mtp180) REVERT: s 52 PHE cc_start: 0.5340 (m-80) cc_final: 0.4939 (m-80) REVERT: s 82 LEU cc_start: 0.4616 (pt) cc_final: 0.4415 (mt) REVERT: t 29 GLN cc_start: 0.4593 (mp10) cc_final: 0.3545 (mt0) REVERT: t 31 ARG cc_start: 0.4006 (OUTLIER) cc_final: 0.3796 (tmm160) REVERT: t 54 ARG cc_start: 0.3963 (ttp-110) cc_final: 0.3537 (tpp-160) REVERT: t 75 GLN cc_start: 0.1752 (OUTLIER) cc_final: 0.1487 (pt0) REVERT: t 89 ASP cc_start: 0.4385 (OUTLIER) cc_final: 0.4065 (t0) REVERT: t 95 TYR cc_start: 0.5183 (m-80) cc_final: 0.4747 (m-80) REVERT: u 29 ARG cc_start: 0.4283 (tmt170) cc_final: 0.3844 (tpp-160) REVERT: u 62 LYS cc_start: 0.3152 (mttt) cc_final: 0.2855 (mtpm) REVERT: u 70 ARG cc_start: 0.4273 (mtt-85) cc_final: 0.3994 (mtm-85) REVERT: u 72 GLU cc_start: 0.4294 (mt-10) cc_final: 0.3696 (tp30) REVERT: u 81 MET cc_start: 0.4716 (mtt) cc_final: 0.4302 (mmm) REVERT: u 93 ARG cc_start: 0.4373 (mtp85) cc_final: 0.4138 (mmt90) REVERT: v 21 PHE cc_start: 0.1806 (OUTLIER) cc_final: 0.1368 (m-80) REVERT: v 24 ARG cc_start: 0.3380 (OUTLIER) cc_final: 0.3105 (ttm-80) REVERT: v 47 LYS cc_start: 0.3194 (mmtm) cc_final: 0.2490 (ptpt) REVERT: v 89 MET cc_start: 0.5940 (mmt) cc_final: 0.5566 (mmp) REVERT: v 90 ARG cc_start: 0.5860 (mtt90) cc_final: 0.4985 (mtt90) REVERT: v 98 LYS cc_start: 0.4892 (mmmt) cc_final: 0.4185 (mmmm) REVERT: w 38 HIS cc_start: 0.5208 (t70) cc_final: 0.4703 (t70) REVERT: w 58 ARG cc_start: 0.5803 (ttt-90) cc_final: 0.5578 (ttp80) REVERT: w 73 LYS cc_start: 0.3289 (mmmt) cc_final: 0.3000 (mmtp) REVERT: w 84 ARG cc_start: 0.3352 (ttt180) cc_final: 0.3079 (tmt90) REVERT: y 4 LYS cc_start: 0.1096 (OUTLIER) cc_final: 0.0513 (tptt) REVERT: y 37 PHE cc_start: 0.5985 (m-80) cc_final: 0.5659 (m-80) REVERT: y 75 LEU cc_start: 0.4084 (tt) cc_final: 0.3870 (tt) REVERT: 1 63 THR cc_start: 0.3295 (OUTLIER) cc_final: 0.2974 (t) REVERT: 1 66 MET cc_start: 0.4594 (mtt) cc_final: 0.3919 (mtt) REVERT: 2 16 LYS cc_start: 0.3538 (OUTLIER) cc_final: 0.3299 (ttpp) REVERT: 3 21 ARG cc_start: 0.3385 (mmt-90) cc_final: 0.3145 (mmm160) REVERT: 3 32 VAL cc_start: 0.5096 (t) cc_final: 0.4574 (m) REVERT: 3 36 GLU cc_start: 0.6515 (tt0) cc_final: 0.6158 (mt-10) REVERT: 3 39 GLU cc_start: 0.5855 (tm-30) cc_final: 0.5138 (pp20) REVERT: 3 40 LYS cc_start: 0.5883 (tptt) cc_final: 0.5212 (mttt) REVERT: 3 46 LYS cc_start: 0.4953 (ttmt) cc_final: 0.4702 (ttmt) REVERT: e 8 LYS cc_start: 0.6207 (mtpt) cc_final: 0.5685 (ptpt) REVERT: e 15 LYS cc_start: 0.6195 (tttm) cc_final: 0.5521 (tptt) REVERT: e 30 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4769 (mm-30) outliers start: 147 outliers final: 86 residues processed: 814 average time/residue: 2.3594 time to fit residues: 2696.4231 Evaluate side-chains 808 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 699 time to evaluate : 5.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 104 ILE Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 18 LYS Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 17 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 304 optimal weight: 10.0000 chunk 813 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 530 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 904 optimal weight: 3.9990 chunk 750 optimal weight: 10.0000 chunk 418 optimal weight: 0.0040 chunk 75 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 474 optimal weight: 5.9990 overall best weight: 5.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 52 ASN b 45 GLN m 78 ASN m 146 ASN ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 GLN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 152207 Z= 0.257 Angle : 0.801 8.486 229001 Z= 0.404 Chirality : 0.043 0.330 29444 Planarity : 0.006 0.092 11367 Dihedral : 23.767 179.851 79419 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Rotamer: Outliers : 3.82 % Allowed : 16.58 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 4751 helix: 0.26 (0.13), residues: 1533 sheet: -0.77 (0.16), residues: 932 loop : -0.89 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 248 HIS 0.008 0.002 HIS 1 69 PHE 0.023 0.003 PHE Q 106 TYR 0.028 0.003 TYR j 213 ARG 0.009 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 724 time to evaluate : 5.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5582 (mttt) cc_final: 0.5057 (mptt) REVERT: C 111 LYS cc_start: 0.5267 (ptmm) cc_final: 0.5031 (ptpp) REVERT: C 125 LYS cc_start: 0.5253 (pttt) cc_final: 0.4909 (ptpt) REVERT: C 133 ARG cc_start: 0.5652 (ptt-90) cc_final: 0.5072 (ttm-80) REVERT: C 163 GLN cc_start: 0.6667 (tt0) cc_final: 0.6074 (mt0) REVERT: C 182 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6571 (ttt180) REVERT: C 183 LYS cc_start: 0.5997 (mttt) cc_final: 0.5583 (mmmt) REVERT: C 199 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6007 (pt0) REVERT: C 201 MET cc_start: 0.7033 (ptt) cc_final: 0.6739 (ptm) REVERT: C 269 ARG cc_start: 0.6026 (ttp-170) cc_final: 0.5313 (ttt-90) REVERT: D 7 LYS cc_start: 0.7004 (ttpp) cc_final: 0.6727 (ttpp) REVERT: D 17 GLU cc_start: 0.4185 (tt0) cc_final: 0.3888 (mp0) REVERT: D 42 ASN cc_start: 0.5058 (t0) cc_final: 0.4778 (t0) REVERT: D 55 LYS cc_start: 0.5085 (ttmm) cc_final: 0.4762 (ttmt) REVERT: D 70 LYS cc_start: 0.5028 (tttt) cc_final: 0.4777 (tptt) REVERT: D 74 GLU cc_start: 0.4876 (tt0) cc_final: 0.4555 (mp0) REVERT: D 99 GLU cc_start: 0.5251 (tp30) cc_final: 0.4644 (mp0) REVERT: D 105 LYS cc_start: 0.5779 (mttt) cc_final: 0.5508 (mmmm) REVERT: D 128 ARG cc_start: 0.7129 (mtt90) cc_final: 0.6335 (mtp180) REVERT: D 131 ASP cc_start: 0.6961 (m-30) cc_final: 0.6515 (m-30) REVERT: D 183 GLU cc_start: 0.4647 (OUTLIER) cc_final: 0.4443 (tp30) REVERT: E 22 ASP cc_start: 0.3895 (t0) cc_final: 0.3452 (p0) REVERT: E 61 ARG cc_start: 0.6903 (ptm160) cc_final: 0.6354 (ptt-90) REVERT: E 106 LYS cc_start: 0.5752 (mtmt) cc_final: 0.5372 (mttt) REVERT: E 170 ARG cc_start: 0.4971 (tpp-160) cc_final: 0.4695 (mmt180) REVERT: E 199 MET cc_start: 0.4361 (ttp) cc_final: 0.4159 (ttm) REVERT: F 94 GLU cc_start: 0.4550 (mp0) cc_final: 0.4259 (tt0) REVERT: F 125 ARG cc_start: 0.3921 (mmt90) cc_final: 0.3671 (mmt90) REVERT: F 133 ARG cc_start: 0.4373 (mtt-85) cc_final: 0.4065 (mtp85) REVERT: G 71 LEU cc_start: 0.5052 (mt) cc_final: 0.4633 (mp) REVERT: G 143 GLN cc_start: 0.6273 (tp-100) cc_final: 0.5966 (tp40) REVERT: G 153 ARG cc_start: 0.4764 (mtt90) cc_final: 0.4455 (ptm-80) REVERT: H 22 LYS cc_start: 0.5684 (mmtp) cc_final: 0.5236 (mttp) REVERT: J 31 GLU cc_start: 0.6377 (tp30) cc_final: 0.5956 (tm-30) REVERT: J 39 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6242 (mmmm) REVERT: J 61 LYS cc_start: 0.6315 (mtmm) cc_final: 0.5569 (mmtt) REVERT: J 85 LYS cc_start: 0.6474 (mttm) cc_final: 0.5912 (mmtm) REVERT: J 90 GLU cc_start: 0.6188 (pt0) cc_final: 0.5270 (tp30) REVERT: J 95 ARG cc_start: 0.5085 (ttm-80) cc_final: 0.4820 (ttp80) REVERT: J 96 ARG cc_start: 0.4574 (mtt180) cc_final: 0.3805 (mmt-90) REVERT: J 99 ARG cc_start: 0.5878 (mmm160) cc_final: 0.5457 (mmp-170) REVERT: J 129 GLU cc_start: 0.5473 (mm-30) cc_final: 0.5137 (tp30) REVERT: J 138 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5634 (mp10) REVERT: K 20 MET cc_start: 0.7435 (ttp) cc_final: 0.7207 (ttm) REVERT: K 53 LYS cc_start: 0.5469 (pttp) cc_final: 0.4867 (tptp) REVERT: K 88 ASN cc_start: 0.5693 (t0) cc_final: 0.5302 (t0) REVERT: K 98 ARG cc_start: 0.5850 (mmt180) cc_final: 0.5103 (mtp180) REVERT: K 113 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.4192 (tpt) REVERT: K 114 LYS cc_start: 0.5030 (tptt) cc_final: 0.4689 (tttm) REVERT: K 121 GLU cc_start: 0.6297 (tt0) cc_final: 0.5965 (tt0) REVERT: L 14 LYS cc_start: 0.5498 (tttt) cc_final: 0.5212 (ttpt) REVERT: L 103 ILE cc_start: 0.5852 (mt) cc_final: 0.5646 (pp) REVERT: L 123 ARG cc_start: 0.4524 (mtm-85) cc_final: 0.4153 (mtt90) REVERT: M 5 LYS cc_start: 0.6080 (mtpt) cc_final: 0.5874 (mtpp) REVERT: M 6 ARG cc_start: 0.5368 (ttt-90) cc_final: 0.4777 (mtp85) REVERT: M 30 SER cc_start: 0.6913 (m) cc_final: 0.6452 (p) REVERT: M 36 VAL cc_start: 0.6806 (t) cc_final: 0.6559 (m) REVERT: M 55 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5870 (ttt90) REVERT: M 59 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5711 (mtm180) REVERT: M 115 GLU cc_start: 0.5598 (mm-30) cc_final: 0.5246 (tt0) REVERT: M 118 LYS cc_start: 0.5822 (mmtm) cc_final: 0.5550 (ttmp) REVERT: M 127 LYS cc_start: 0.5992 (ttmt) cc_final: 0.5366 (tptp) REVERT: M 133 LYS cc_start: 0.5438 (ttpp) cc_final: 0.5152 (tttm) REVERT: M 136 MET cc_start: 0.3465 (mtp) cc_final: 0.3151 (mtt) REVERT: N 73 ASN cc_start: 0.6259 (m-40) cc_final: 0.5877 (m-40) REVERT: O 16 ARG cc_start: 0.5782 (mmp80) cc_final: 0.5309 (mmt90) REVERT: O 17 LYS cc_start: 0.5213 (mmtp) cc_final: 0.4926 (tppt) REVERT: O 19 GLN cc_start: 0.5639 (tm-30) cc_final: 0.5415 (tm-30) REVERT: O 91 SER cc_start: 0.6127 (m) cc_final: 0.5514 (p) REVERT: P 6 LYS cc_start: 0.5187 (tptt) cc_final: 0.4978 (mtmt) REVERT: P 7 GLN cc_start: 0.5733 (tt0) cc_final: 0.4956 (mm-40) REVERT: P 13 MET cc_start: 0.5613 (mtp) cc_final: 0.5268 (mmm) REVERT: P 33 VAL cc_start: 0.4679 (t) cc_final: 0.4245 (m) REVERT: P 89 ARG cc_start: 0.5665 (mtm-85) cc_final: 0.5005 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6158 (tpm170) cc_final: 0.5470 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6356 (mtpp) cc_final: 0.5998 (mtmp) REVERT: Q 84 LYS cc_start: 0.5545 (ttpp) cc_final: 0.4938 (mmtm) REVERT: Q 87 SER cc_start: 0.5806 (OUTLIER) cc_final: 0.5572 (m) REVERT: Q 89 GLU cc_start: 0.5526 (mt-10) cc_final: 0.4886 (mm-30) REVERT: R 6 GLN cc_start: 0.5641 (tt0) cc_final: 0.5217 (pt0) REVERT: R 13 ARG cc_start: 0.6450 (ttp80) cc_final: 0.5819 (ttp-170) REVERT: R 34 GLU cc_start: 0.5198 (mt-10) cc_final: 0.4755 (mp0) REVERT: R 60 LYS cc_start: 0.4578 (mttp) cc_final: 0.4317 (mtpt) REVERT: R 86 GLN cc_start: 0.6580 (pt0) cc_final: 0.6230 (pm20) REVERT: S 11 ARG cc_start: 0.5753 (mmt-90) cc_final: 0.5328 (mmm-85) REVERT: S 12 SER cc_start: 0.6748 (t) cc_final: 0.6439 (p) REVERT: T 5 GLU cc_start: 0.4747 (mp0) cc_final: 0.4542 (tt0) REVERT: T 8 LEU cc_start: 0.6284 (mt) cc_final: 0.5968 (mt) REVERT: T 56 GLU cc_start: 0.5472 (tp30) cc_final: 0.5032 (tp30) REVERT: T 69 ARG cc_start: 0.4406 (ptp-170) cc_final: 0.4058 (mtp85) REVERT: T 73 ARG cc_start: 0.3095 (tpt170) cc_final: 0.2764 (ttp-110) REVERT: U 9 ASP cc_start: 0.5174 (m-30) cc_final: 0.4607 (m-30) REVERT: U 26 LYS cc_start: 0.5011 (mmmt) cc_final: 0.4652 (mttp) REVERT: U 46 GLN cc_start: 0.4901 (pt0) cc_final: 0.4609 (mt0) REVERT: V 43 ASP cc_start: 0.5834 (t0) cc_final: 0.5213 (m-30) REVERT: V 48 MET cc_start: 0.5441 (tpt) cc_final: 0.4960 (tpt) REVERT: V 61 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4735 (mt) REVERT: V 71 LYS cc_start: 0.5254 (mmmt) cc_final: 0.5027 (mmtt) REVERT: V 82 TYR cc_start: 0.6038 (p90) cc_final: 0.5760 (p90) REVERT: W 29 GLU cc_start: 0.6576 (tt0) cc_final: 0.6165 (mt-10) REVERT: W 39 ARG cc_start: 0.6466 (mtt-85) cc_final: 0.5889 (mtm180) REVERT: W 44 LYS cc_start: 0.6622 (tttt) cc_final: 0.6319 (mtpt) REVERT: W 66 LYS cc_start: 0.6680 (mttt) cc_final: 0.6098 (mtpt) REVERT: W 72 LYS cc_start: 0.5341 (mmmt) cc_final: 0.4972 (mmtm) REVERT: W 78 LYS cc_start: 0.6216 (mttt) cc_final: 0.5713 (mtmm) REVERT: Y 29 ARG cc_start: 0.5077 (mtm-85) cc_final: 0.4593 (ttm-80) REVERT: Y 46 VAL cc_start: 0.5482 (t) cc_final: 0.5229 (p) REVERT: Z 56 LYS cc_start: 0.5643 (tmtt) cc_final: 0.5116 (ptmm) REVERT: a 37 LYS cc_start: 0.6082 (mtmm) cc_final: 0.5723 (mmmt) REVERT: a 52 ARG cc_start: 0.4856 (ptp90) cc_final: 0.4440 (ttt180) REVERT: b 7 GLU cc_start: 0.5718 (mt-10) cc_final: 0.5411 (tt0) REVERT: b 10 LYS cc_start: 0.4937 (mptt) cc_final: 0.4068 (mmtp) REVERT: b 33 LYS cc_start: 0.5021 (mmtt) cc_final: 0.4690 (mmmm) REVERT: b 35 GLU cc_start: 0.5964 (mt-10) cc_final: 0.5555 (tt0) REVERT: b 44 ARG cc_start: 0.5627 (mtp180) cc_final: 0.4309 (mtp85) REVERT: c 12 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6385 (ttt90) REVERT: c 25 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5988 (tmmt) REVERT: d 16 LYS cc_start: 0.6256 (tptm) cc_final: 0.5786 (tptt) REVERT: j 21 ARG cc_start: 0.3171 (OUTLIER) cc_final: 0.2413 (ptt180) REVERT: j 47 VAL cc_start: 0.3604 (t) cc_final: 0.3392 (t) REVERT: j 49 MET cc_start: 0.3600 (mtm) cc_final: 0.3197 (mtm) REVERT: j 50 PHE cc_start: 0.3212 (OUTLIER) cc_final: 0.2817 (p90) REVERT: j 64 LYS cc_start: 0.3084 (mtpp) cc_final: 0.2740 (ptpp) REVERT: j 105 LYS cc_start: 0.5079 (tttt) cc_final: 0.4608 (tppt) REVERT: j 169 GLU cc_start: 0.5557 (mm-30) cc_final: 0.5331 (mm-30) REVERT: j 212 LEU cc_start: 0.3346 (tt) cc_final: 0.3058 (tp) REVERT: m 13 GLU cc_start: 0.4996 (pt0) cc_final: 0.4530 (pm20) REVERT: m 26 LYS cc_start: 0.5012 (tptp) cc_final: 0.4742 (ttpt) REVERT: m 30 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.6174 (mm) REVERT: m 43 ASN cc_start: 0.4580 (t0) cc_final: 0.4300 (m-40) REVERT: m 45 ARG cc_start: 0.4734 (mmm-85) cc_final: 0.4037 (mmm-85) REVERT: m 55 GLU cc_start: 0.4594 (mm-30) cc_final: 0.3886 (pt0) REVERT: m 61 GLN cc_start: 0.5532 (tt0) cc_final: 0.5076 (tp40) REVERT: m 64 MET cc_start: 0.5564 (mmt) cc_final: 0.5228 (mmt) REVERT: m 65 GLU cc_start: 0.5556 (tt0) cc_final: 0.5163 (tp30) REVERT: m 73 ASN cc_start: 0.5221 (m110) cc_final: 0.4779 (m-40) REVERT: m 93 ARG cc_start: 0.5524 (mpp-170) cc_final: 0.5282 (mtt90) REVERT: m 142 ASP cc_start: 0.4152 (m-30) cc_final: 0.3865 (t0) REVERT: m 156 LYS cc_start: 0.4366 (mtmm) cc_final: 0.4063 (mtmm) REVERT: n 79 ARG cc_start: 0.3739 (ttm-80) cc_final: 0.3489 (ttm170) REVERT: o 74 GLU cc_start: 0.4693 (pt0) cc_final: 0.4118 (tt0) REVERT: o 76 LYS cc_start: 0.3286 (mmmt) cc_final: 0.3072 (mptt) REVERT: o 106 GLU cc_start: 0.4908 (tt0) cc_final: 0.4340 (mm-30) REVERT: o 123 GLU cc_start: 0.4494 (tp30) cc_final: 0.3887 (tm-30) REVERT: o 144 MET cc_start: 0.4957 (mmm) cc_final: 0.4699 (mtp) REVERT: o 146 GLU cc_start: 0.4272 (mm-30) cc_final: 0.3888 (tm-30) REVERT: p 40 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5173 (mp) REVERT: p 69 LYS cc_start: 0.3993 (OUTLIER) cc_final: 0.3647 (tppt) REVERT: p 88 ARG cc_start: 0.3984 (mtm180) cc_final: 0.3715 (mtm110) REVERT: p 94 LYS cc_start: 0.4395 (ptpt) cc_final: 0.4187 (mtmm) REVERT: q 65 ILE cc_start: 0.4259 (mt) cc_final: 0.4039 (mp) REVERT: q 85 ARG cc_start: 0.4156 (OUTLIER) cc_final: 0.2510 (mpt-90) REVERT: q 105 THR cc_start: 0.4993 (t) cc_final: 0.4650 (t) REVERT: q 119 ARG cc_start: 0.4937 (mtm110) cc_final: 0.4365 (mtt180) REVERT: q 124 ARG cc_start: 0.6032 (ttm-80) cc_final: 0.5662 (mtp-110) REVERT: s 52 PHE cc_start: 0.5308 (m-80) cc_final: 0.4967 (m-80) REVERT: s 82 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4398 (mt) REVERT: t 29 GLN cc_start: 0.4649 (mp10) cc_final: 0.3482 (mt0) REVERT: t 31 ARG cc_start: 0.4025 (OUTLIER) cc_final: 0.3787 (tmm160) REVERT: t 54 ARG cc_start: 0.3968 (ttp-110) cc_final: 0.3575 (tpp-160) REVERT: t 75 GLN cc_start: 0.1494 (OUTLIER) cc_final: 0.1130 (pt0) REVERT: t 89 ASP cc_start: 0.4505 (OUTLIER) cc_final: 0.4173 (t0) REVERT: t 95 TYR cc_start: 0.5206 (m-80) cc_final: 0.4763 (m-80) REVERT: u 62 LYS cc_start: 0.3294 (mttt) cc_final: 0.2986 (mtpm) REVERT: u 70 ARG cc_start: 0.4208 (mtt-85) cc_final: 0.3966 (mtm-85) REVERT: u 72 GLU cc_start: 0.4393 (mt-10) cc_final: 0.3691 (tp30) REVERT: u 81 MET cc_start: 0.4793 (mtt) cc_final: 0.4308 (mmm) REVERT: u 93 ARG cc_start: 0.4357 (mtp85) cc_final: 0.4137 (mmt90) REVERT: v 21 PHE cc_start: 0.1768 (OUTLIER) cc_final: 0.1333 (m-80) REVERT: v 24 ARG cc_start: 0.3399 (OUTLIER) cc_final: 0.2804 (tpm170) REVERT: v 47 LYS cc_start: 0.3204 (mmtm) cc_final: 0.2510 (ptpt) REVERT: v 89 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5700 (mmp) REVERT: v 90 ARG cc_start: 0.5852 (mtt90) cc_final: 0.4975 (mtt90) REVERT: v 98 LYS cc_start: 0.5016 (mmmt) cc_final: 0.4294 (mmmm) REVERT: w 38 HIS cc_start: 0.5246 (t70) cc_final: 0.4770 (t70) REVERT: w 58 ARG cc_start: 0.5872 (ttt-90) cc_final: 0.5627 (ttp80) REVERT: w 73 LYS cc_start: 0.3338 (mmmt) cc_final: 0.3042 (mmtp) REVERT: w 84 ARG cc_start: 0.3232 (ttt180) cc_final: 0.3004 (tmt90) REVERT: y 37 PHE cc_start: 0.5954 (m-80) cc_final: 0.5587 (m-80) REVERT: 1 66 MET cc_start: 0.4553 (mtt) cc_final: 0.3740 (mtt) REVERT: 1 81 ARG cc_start: 0.4014 (mpp80) cc_final: 0.3661 (mpp80) REVERT: 3 32 VAL cc_start: 0.5180 (t) cc_final: 0.4663 (m) REVERT: 3 34 ARG cc_start: 0.5706 (mmt90) cc_final: 0.5393 (mpt180) REVERT: 3 36 GLU cc_start: 0.6550 (tt0) cc_final: 0.6128 (mt-10) REVERT: 3 39 GLU cc_start: 0.5837 (tm-30) cc_final: 0.5162 (pp20) REVERT: 3 40 LYS cc_start: 0.5932 (tptt) cc_final: 0.5303 (tttp) REVERT: 3 46 LYS cc_start: 0.4847 (ttmt) cc_final: 0.4591 (ttpt) REVERT: e 8 LYS cc_start: 0.6116 (mtpt) cc_final: 0.5648 (ptpt) REVERT: e 15 LYS cc_start: 0.6163 (tttm) cc_final: 0.5501 (tptt) REVERT: e 30 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.4780 (mm-30) outliers start: 151 outliers final: 103 residues processed: 817 average time/residue: 2.3255 time to fit residues: 2676.3849 Evaluate side-chains 835 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 709 time to evaluate : 5.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 78 GLU Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain m residue 159 LYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 LYS Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain s residue 18 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 82 LEU Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain v residue 89 MET Chi-restraints excluded: chain w residue 3 LEU Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 17 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 70 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 872 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 515 optimal weight: 1.9990 chunk 660 optimal weight: 20.0000 chunk 511 optimal weight: 0.9990 chunk 761 optimal weight: 10.0000 chunk 505 optimal weight: 8.9990 chunk 901 optimal weight: 2.9990 chunk 563 optimal weight: 7.9990 chunk 549 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN b 45 GLN m 78 ASN m 146 ASN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 152207 Z= 0.202 Angle : 0.698 8.749 229001 Z= 0.358 Chirality : 0.039 0.322 29444 Planarity : 0.006 0.073 11367 Dihedral : 23.687 179.843 79419 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.29 % Favored : 95.56 % Rotamer: Outliers : 3.77 % Allowed : 17.13 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 4751 helix: 0.38 (0.13), residues: 1553 sheet: -0.70 (0.16), residues: 916 loop : -0.86 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 248 HIS 0.007 0.002 HIS V 44 PHE 0.021 0.002 PHE j 50 TYR 0.024 0.002 TYR j 213 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 709 time to evaluate : 5.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5577 (mttt) cc_final: 0.5051 (mptt) REVERT: C 111 LYS cc_start: 0.5358 (ptmm) cc_final: 0.5124 (ptpp) REVERT: C 125 LYS cc_start: 0.5262 (pttt) cc_final: 0.4917 (ptpt) REVERT: C 133 ARG cc_start: 0.5712 (ptt-90) cc_final: 0.5102 (ttm-80) REVERT: C 163 GLN cc_start: 0.6671 (tt0) cc_final: 0.6078 (mt0) REVERT: C 182 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6571 (ttt180) REVERT: C 183 LYS cc_start: 0.6039 (mttt) cc_final: 0.5634 (mmmt) REVERT: C 199 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6000 (pt0) REVERT: C 201 MET cc_start: 0.7011 (ptt) cc_final: 0.6724 (ptm) REVERT: C 269 ARG cc_start: 0.6065 (ttp-170) cc_final: 0.5350 (ttt-90) REVERT: D 7 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6720 (ttpp) REVERT: D 17 GLU cc_start: 0.4226 (tt0) cc_final: 0.3944 (mp0) REVERT: D 42 ASN cc_start: 0.4991 (t0) cc_final: 0.4730 (t0) REVERT: D 55 LYS cc_start: 0.5098 (ttmm) cc_final: 0.4760 (ttmt) REVERT: D 70 LYS cc_start: 0.5056 (tttt) cc_final: 0.4759 (tptt) REVERT: D 99 GLU cc_start: 0.5210 (tp30) cc_final: 0.4638 (mp0) REVERT: D 105 LYS cc_start: 0.5909 (mttt) cc_final: 0.5540 (mmmt) REVERT: D 128 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6330 (mtp180) REVERT: D 131 ASP cc_start: 0.6843 (m-30) cc_final: 0.6385 (m-30) REVERT: D 183 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.4401 (tp30) REVERT: E 22 ASP cc_start: 0.3877 (t0) cc_final: 0.3432 (p0) REVERT: E 61 ARG cc_start: 0.6908 (ptm160) cc_final: 0.6366 (ptt-90) REVERT: E 106 LYS cc_start: 0.5755 (mtmt) cc_final: 0.5371 (mttt) REVERT: E 170 ARG cc_start: 0.4880 (tpp-160) cc_final: 0.4596 (tpp80) REVERT: E 199 MET cc_start: 0.4388 (ttp) cc_final: 0.4179 (ttm) REVERT: F 38 MET cc_start: 0.5556 (mtm) cc_final: 0.5308 (mtm) REVERT: F 89 VAL cc_start: 0.6386 (OUTLIER) cc_final: 0.5963 (m) REVERT: F 94 GLU cc_start: 0.4607 (mp0) cc_final: 0.4348 (tt0) REVERT: F 125 ARG cc_start: 0.4027 (mmt90) cc_final: 0.3768 (mmt90) REVERT: F 133 ARG cc_start: 0.4374 (mtt-85) cc_final: 0.4065 (mtp85) REVERT: F 150 ARG cc_start: 0.3939 (mtm180) cc_final: 0.3230 (mpp-170) REVERT: G 71 LEU cc_start: 0.5115 (mt) cc_final: 0.4678 (mp) REVERT: G 143 GLN cc_start: 0.6241 (tp-100) cc_final: 0.5983 (tp40) REVERT: G 153 ARG cc_start: 0.4753 (mtt90) cc_final: 0.4444 (ptm-80) REVERT: H 22 LYS cc_start: 0.5818 (mmtp) cc_final: 0.5396 (mttp) REVERT: J 31 GLU cc_start: 0.6397 (tp30) cc_final: 0.6008 (tm-30) REVERT: J 39 LYS cc_start: 0.6609 (mtpp) cc_final: 0.6235 (mmmm) REVERT: J 61 LYS cc_start: 0.6312 (mtmm) cc_final: 0.5568 (mmtm) REVERT: J 85 LYS cc_start: 0.6455 (mttm) cc_final: 0.5884 (mmtm) REVERT: J 90 GLU cc_start: 0.6204 (pt0) cc_final: 0.5303 (tp30) REVERT: J 95 ARG cc_start: 0.5142 (ttm-80) cc_final: 0.4907 (ttp80) REVERT: J 96 ARG cc_start: 0.4597 (mtt180) cc_final: 0.3813 (mmt180) REVERT: J 99 ARG cc_start: 0.5878 (mmm160) cc_final: 0.5454 (mmp-170) REVERT: J 129 GLU cc_start: 0.5507 (mm-30) cc_final: 0.5162 (tp30) REVERT: J 138 GLN cc_start: 0.5930 (OUTLIER) cc_final: 0.5652 (mp10) REVERT: K 20 MET cc_start: 0.7429 (ttp) cc_final: 0.7176 (ttm) REVERT: K 53 LYS cc_start: 0.5545 (pttp) cc_final: 0.4922 (tptp) REVERT: K 88 ASN cc_start: 0.5803 (t0) cc_final: 0.5422 (t0) REVERT: K 113 MET cc_start: 0.4422 (OUTLIER) cc_final: 0.4201 (tpt) REVERT: K 114 LYS cc_start: 0.5025 (tptt) cc_final: 0.4679 (tttm) REVERT: K 121 GLU cc_start: 0.6298 (tt0) cc_final: 0.6002 (tt0) REVERT: L 14 LYS cc_start: 0.5492 (tttt) cc_final: 0.5219 (ttpt) REVERT: L 17 LYS cc_start: 0.6649 (mttt) cc_final: 0.6269 (mttm) REVERT: L 103 ILE cc_start: 0.5813 (mt) cc_final: 0.5597 (pp) REVERT: L 123 ARG cc_start: 0.4383 (mtm-85) cc_final: 0.4086 (mtt90) REVERT: M 5 LYS cc_start: 0.6077 (mtpt) cc_final: 0.5864 (mtpp) REVERT: M 6 ARG cc_start: 0.5362 (ttt-90) cc_final: 0.4790 (mtp85) REVERT: M 30 SER cc_start: 0.6887 (m) cc_final: 0.6494 (p) REVERT: M 36 VAL cc_start: 0.6785 (t) cc_final: 0.6546 (m) REVERT: M 55 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5892 (ttt90) REVERT: M 59 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5709 (mtm180) REVERT: M 115 GLU cc_start: 0.5543 (mm-30) cc_final: 0.5186 (tt0) REVERT: M 118 LYS cc_start: 0.5813 (mmtm) cc_final: 0.5555 (ttmp) REVERT: M 127 LYS cc_start: 0.6045 (ttmt) cc_final: 0.5434 (tptp) REVERT: M 136 MET cc_start: 0.3499 (mtp) cc_final: 0.2285 (mpt) REVERT: N 73 ASN cc_start: 0.6316 (m-40) cc_final: 0.5935 (m-40) REVERT: O 16 ARG cc_start: 0.5745 (mmp80) cc_final: 0.5273 (mmt90) REVERT: O 17 LYS cc_start: 0.5204 (mmtp) cc_final: 0.4923 (tppt) REVERT: O 19 GLN cc_start: 0.5608 (tm-30) cc_final: 0.5368 (tm-30) REVERT: O 91 SER cc_start: 0.6067 (m) cc_final: 0.5456 (p) REVERT: P 6 LYS cc_start: 0.5169 (tptt) cc_final: 0.4964 (mtmt) REVERT: P 7 GLN cc_start: 0.5727 (tt0) cc_final: 0.4949 (mm-40) REVERT: P 13 MET cc_start: 0.5591 (mtp) cc_final: 0.5224 (mmm) REVERT: P 33 VAL cc_start: 0.4694 (t) cc_final: 0.4268 (m) REVERT: P 89 ARG cc_start: 0.5683 (mtm-85) cc_final: 0.5020 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6169 (tpm170) cc_final: 0.5469 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6348 (mtpp) cc_final: 0.6000 (mtmp) REVERT: Q 84 LYS cc_start: 0.5533 (ttpp) cc_final: 0.4943 (mmtm) REVERT: Q 89 GLU cc_start: 0.5522 (mt-10) cc_final: 0.4882 (mm-30) REVERT: R 6 GLN cc_start: 0.5629 (tt0) cc_final: 0.5205 (pt0) REVERT: R 13 ARG cc_start: 0.6437 (ttp80) cc_final: 0.5798 (ttp-170) REVERT: R 34 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4779 (mp0) REVERT: R 60 LYS cc_start: 0.4508 (mttp) cc_final: 0.4200 (mtpt) REVERT: R 86 GLN cc_start: 0.6587 (pt0) cc_final: 0.6235 (pm20) REVERT: S 11 ARG cc_start: 0.5829 (mmt-90) cc_final: 0.5287 (mmm-85) REVERT: S 12 SER cc_start: 0.6728 (t) cc_final: 0.6438 (p) REVERT: T 5 GLU cc_start: 0.4698 (mp0) cc_final: 0.4490 (tt0) REVERT: T 8 LEU cc_start: 0.6249 (mt) cc_final: 0.5918 (mt) REVERT: T 56 GLU cc_start: 0.5470 (tp30) cc_final: 0.5005 (tp30) REVERT: T 69 ARG cc_start: 0.4418 (ptp-170) cc_final: 0.4055 (mtp85) REVERT: T 73 ARG cc_start: 0.3242 (tpt170) cc_final: 0.2874 (ttp-110) REVERT: U 9 ASP cc_start: 0.5111 (m-30) cc_final: 0.4579 (m-30) REVERT: U 26 LYS cc_start: 0.4985 (mmmt) cc_final: 0.4635 (mttp) REVERT: U 46 GLN cc_start: 0.5004 (pt0) cc_final: 0.4693 (mt0) REVERT: V 43 ASP cc_start: 0.5798 (t0) cc_final: 0.5181 (m-30) REVERT: V 48 MET cc_start: 0.5390 (tpt) cc_final: 0.4850 (tpt) REVERT: V 61 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4731 (mt) REVERT: V 71 LYS cc_start: 0.5180 (mmmt) cc_final: 0.4968 (mmtt) REVERT: W 29 GLU cc_start: 0.6576 (tt0) cc_final: 0.6151 (mt-10) REVERT: W 39 ARG cc_start: 0.6461 (mtt-85) cc_final: 0.5883 (mtm180) REVERT: W 44 LYS cc_start: 0.6581 (tttt) cc_final: 0.6275 (mtpt) REVERT: W 66 LYS cc_start: 0.6675 (mttt) cc_final: 0.6102 (mtpt) REVERT: W 72 LYS cc_start: 0.5317 (mmmt) cc_final: 0.4940 (mmtm) REVERT: W 78 LYS cc_start: 0.6274 (mttt) cc_final: 0.5789 (mtmm) REVERT: Y 13 GLU cc_start: 0.4842 (mt-10) cc_final: 0.4640 (mm-30) REVERT: Y 14 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4576 (mp) REVERT: Y 29 ARG cc_start: 0.5112 (mtm-85) cc_final: 0.4569 (ttm-80) REVERT: Y 46 VAL cc_start: 0.5605 (t) cc_final: 0.5330 (p) REVERT: Z 56 LYS cc_start: 0.5674 (tmtt) cc_final: 0.5136 (ptmm) REVERT: a 37 LYS cc_start: 0.6078 (mtmm) cc_final: 0.5708 (mmmt) REVERT: a 52 ARG cc_start: 0.4879 (ptp90) cc_final: 0.4437 (ttt180) REVERT: b 7 GLU cc_start: 0.5879 (mt-10) cc_final: 0.5483 (tt0) REVERT: b 10 LYS cc_start: 0.4937 (mptt) cc_final: 0.4532 (ptpt) REVERT: b 33 LYS cc_start: 0.4997 (mmtt) cc_final: 0.4666 (mmmm) REVERT: b 35 GLU cc_start: 0.5975 (mt-10) cc_final: 0.5562 (tt0) REVERT: b 44 ARG cc_start: 0.5619 (mtp180) cc_final: 0.4305 (mtp85) REVERT: c 12 ARG cc_start: 0.7001 (ttp80) cc_final: 0.6385 (ttt90) REVERT: c 25 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5970 (tmmt) REVERT: d 16 LYS cc_start: 0.6411 (tptm) cc_final: 0.6050 (tptt) REVERT: j 21 ARG cc_start: 0.3133 (OUTLIER) cc_final: 0.2372 (pmm-80) REVERT: j 47 VAL cc_start: 0.3605 (t) cc_final: 0.3387 (t) REVERT: j 49 MET cc_start: 0.3625 (mtm) cc_final: 0.3304 (mtm) REVERT: j 50 PHE cc_start: 0.3194 (OUTLIER) cc_final: 0.2817 (p90) REVERT: j 64 LYS cc_start: 0.2890 (mtpp) cc_final: 0.2552 (ptpp) REVERT: j 105 LYS cc_start: 0.5147 (tttt) cc_final: 0.4590 (tppt) REVERT: j 169 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5391 (mm-30) REVERT: j 212 LEU cc_start: 0.3348 (tt) cc_final: 0.3043 (tp) REVERT: j 214 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.4228 (mp) REVERT: m 13 GLU cc_start: 0.4987 (pt0) cc_final: 0.4509 (pm20) REVERT: m 26 LYS cc_start: 0.5031 (tptp) cc_final: 0.4797 (ttpt) REVERT: m 30 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6201 (mm) REVERT: m 43 ASN cc_start: 0.4656 (t0) cc_final: 0.4373 (m-40) REVERT: m 45 ARG cc_start: 0.4802 (mmm-85) cc_final: 0.4097 (mmm-85) REVERT: m 55 GLU cc_start: 0.4619 (mm-30) cc_final: 0.3910 (pt0) REVERT: m 61 GLN cc_start: 0.5587 (tt0) cc_final: 0.5150 (tp40) REVERT: m 64 MET cc_start: 0.5430 (mmt) cc_final: 0.5130 (mmt) REVERT: m 65 GLU cc_start: 0.5585 (tt0) cc_final: 0.5192 (tp30) REVERT: m 73 ASN cc_start: 0.5348 (m110) cc_final: 0.4984 (m-40) REVERT: m 93 ARG cc_start: 0.5519 (mpp-170) cc_final: 0.5261 (mtt90) REVERT: m 142 ASP cc_start: 0.4068 (m-30) cc_final: 0.3788 (t0) REVERT: m 156 LYS cc_start: 0.4270 (mtmm) cc_final: 0.3986 (mtmm) REVERT: n 79 ARG cc_start: 0.3742 (ttm-80) cc_final: 0.3501 (ttm170) REVERT: o 74 GLU cc_start: 0.4765 (pt0) cc_final: 0.4117 (tt0) REVERT: o 76 LYS cc_start: 0.3253 (mmmt) cc_final: 0.3025 (mptt) REVERT: o 106 GLU cc_start: 0.4927 (tt0) cc_final: 0.4320 (mm-30) REVERT: o 123 GLU cc_start: 0.4492 (tp30) cc_final: 0.3888 (tm-30) REVERT: o 146 GLU cc_start: 0.4345 (mm-30) cc_final: 0.3939 (tm-30) REVERT: p 40 LEU cc_start: 0.5248 (OUTLIER) cc_final: 0.5011 (mp) REVERT: p 69 LYS cc_start: 0.4004 (OUTLIER) cc_final: 0.3656 (tppt) REVERT: q 65 ILE cc_start: 0.4334 (mt) cc_final: 0.4105 (mp) REVERT: q 85 ARG cc_start: 0.4173 (OUTLIER) cc_final: 0.2470 (mpt-90) REVERT: q 106 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.3654 (tpt90) REVERT: q 119 ARG cc_start: 0.4856 (mtm110) cc_final: 0.4279 (mtt180) REVERT: q 124 ARG cc_start: 0.5859 (ttm-80) cc_final: 0.5447 (mtp-110) REVERT: s 52 PHE cc_start: 0.5272 (m-80) cc_final: 0.4941 (m-80) REVERT: t 29 GLN cc_start: 0.4719 (mp10) cc_final: 0.3545 (mt0) REVERT: t 31 ARG cc_start: 0.4020 (OUTLIER) cc_final: 0.3773 (tmm160) REVERT: t 54 ARG cc_start: 0.3956 (ttp-110) cc_final: 0.3540 (tpp-160) REVERT: t 75 GLN cc_start: 0.1617 (OUTLIER) cc_final: 0.1248 (pt0) REVERT: t 89 ASP cc_start: 0.4346 (OUTLIER) cc_final: 0.4046 (t0) REVERT: t 95 TYR cc_start: 0.5143 (m-80) cc_final: 0.4676 (m-80) REVERT: u 62 LYS cc_start: 0.3185 (mttt) cc_final: 0.2887 (mtpm) REVERT: u 70 ARG cc_start: 0.4200 (mtt-85) cc_final: 0.4000 (mtm-85) REVERT: u 72 GLU cc_start: 0.4332 (mt-10) cc_final: 0.3664 (tp30) REVERT: u 81 MET cc_start: 0.4783 (mtt) cc_final: 0.4347 (mmm) REVERT: u 93 ARG cc_start: 0.4372 (mtp85) cc_final: 0.4152 (mmt90) REVERT: v 21 PHE cc_start: 0.1831 (OUTLIER) cc_final: 0.1354 (m-80) REVERT: v 24 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.3118 (ttm-80) REVERT: v 47 LYS cc_start: 0.3153 (mmtm) cc_final: 0.2472 (ptpt) REVERT: v 89 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5580 (mmp) REVERT: v 90 ARG cc_start: 0.5797 (mtt90) cc_final: 0.4918 (mtt90) REVERT: v 98 LYS cc_start: 0.5002 (mmmt) cc_final: 0.4283 (mmmm) REVERT: w 38 HIS cc_start: 0.5246 (t70) cc_final: 0.4789 (t70) REVERT: w 58 ARG cc_start: 0.5869 (ttt-90) cc_final: 0.5624 (ttp80) REVERT: w 73 LYS cc_start: 0.3345 (mmmt) cc_final: 0.3044 (mmtp) REVERT: w 84 ARG cc_start: 0.3261 (ttt180) cc_final: 0.3028 (tmt90) REVERT: y 37 PHE cc_start: 0.5958 (m-80) cc_final: 0.5613 (m-80) REVERT: 1 37 ARG cc_start: 0.4942 (ptp90) cc_final: 0.4412 (ptt-90) REVERT: 1 63 THR cc_start: 0.3371 (OUTLIER) cc_final: 0.3129 (t) REVERT: 1 66 MET cc_start: 0.4368 (mtt) cc_final: 0.3701 (mtt) REVERT: 1 81 ARG cc_start: 0.3930 (mpp80) cc_final: 0.3587 (mpp80) REVERT: 2 16 LYS cc_start: 0.3631 (OUTLIER) cc_final: 0.3390 (ttpp) REVERT: 3 32 VAL cc_start: 0.5108 (t) cc_final: 0.4605 (m) REVERT: 3 36 GLU cc_start: 0.6633 (tt0) cc_final: 0.6200 (mm-30) REVERT: 3 39 GLU cc_start: 0.5779 (tm-30) cc_final: 0.5053 (pp20) REVERT: 3 40 LYS cc_start: 0.5892 (tptt) cc_final: 0.5203 (mttt) REVERT: 3 46 LYS cc_start: 0.4891 (ttmt) cc_final: 0.4628 (ttpt) REVERT: e 8 LYS cc_start: 0.6182 (mtpt) cc_final: 0.5720 (ptpt) REVERT: e 15 LYS cc_start: 0.6199 (tttm) cc_final: 0.5525 (tptt) REVERT: e 30 GLU cc_start: 0.5027 (OUTLIER) cc_final: 0.4805 (mm-30) outliers start: 149 outliers final: 99 residues processed: 799 average time/residue: 2.3400 time to fit residues: 2631.7858 Evaluate side-chains 826 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 700 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain j residue 214 LEU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain m residue 159 LYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain q residue 105 THR Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain v residue 89 MET Chi-restraints excluded: chain w residue 3 LEU Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 17 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 ARG Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 557 optimal weight: 20.0000 chunk 359 optimal weight: 0.0870 chunk 538 optimal weight: 0.9980 chunk 271 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 572 optimal weight: 0.6980 chunk 613 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 708 optimal weight: 30.0000 overall best weight: 5.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN U 45 HIS b 45 GLN m 78 ASN m 146 ASN ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 152207 Z= 0.257 Angle : 0.801 9.790 229001 Z= 0.403 Chirality : 0.043 0.337 29444 Planarity : 0.007 0.089 11367 Dihedral : 23.762 179.384 79419 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 3.95 % Allowed : 17.21 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 4751 helix: 0.20 (0.13), residues: 1531 sheet: -0.78 (0.16), residues: 929 loop : -0.91 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 248 HIS 0.009 0.002 HIS K 29 PHE 0.024 0.003 PHE 1 10 TYR 0.027 0.003 TYR j 213 ARG 0.009 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 721 time to evaluate : 5.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5572 (mttt) cc_final: 0.5047 (mptt) REVERT: C 13 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5296 (mmm160) REVERT: C 111 LYS cc_start: 0.5338 (ptmm) cc_final: 0.5092 (ptpp) REVERT: C 125 LYS cc_start: 0.5262 (pttt) cc_final: 0.4919 (ptpt) REVERT: C 133 ARG cc_start: 0.5657 (ptt-90) cc_final: 0.5078 (ttm-80) REVERT: C 163 GLN cc_start: 0.6667 (tt0) cc_final: 0.6073 (mt0) REVERT: C 182 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6571 (ttt180) REVERT: C 183 LYS cc_start: 0.6000 (mttt) cc_final: 0.5614 (mmmt) REVERT: C 199 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5986 (pt0) REVERT: C 201 MET cc_start: 0.7029 (ptt) cc_final: 0.6736 (ptm) REVERT: C 269 ARG cc_start: 0.6035 (ttp-170) cc_final: 0.5348 (ttt-90) REVERT: D 7 LYS cc_start: 0.6993 (ttpp) cc_final: 0.6712 (ttpp) REVERT: D 17 GLU cc_start: 0.4186 (tt0) cc_final: 0.3878 (mp0) REVERT: D 42 ASN cc_start: 0.4957 (t0) cc_final: 0.4668 (t0) REVERT: D 55 LYS cc_start: 0.5084 (ttmm) cc_final: 0.4735 (ttmt) REVERT: D 70 LYS cc_start: 0.5023 (tttt) cc_final: 0.4777 (tptt) REVERT: D 74 GLU cc_start: 0.4894 (tt0) cc_final: 0.4579 (mp0) REVERT: D 91 THR cc_start: 0.5395 (m) cc_final: 0.4937 (p) REVERT: D 99 GLU cc_start: 0.5155 (tp30) cc_final: 0.4591 (mp0) REVERT: D 105 LYS cc_start: 0.5798 (mttt) cc_final: 0.5545 (mmmm) REVERT: D 128 ARG cc_start: 0.7122 (mtt90) cc_final: 0.6331 (mtp180) REVERT: D 131 ASP cc_start: 0.6946 (m-30) cc_final: 0.6492 (m-30) REVERT: D 183 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.4445 (tp30) REVERT: E 22 ASP cc_start: 0.3930 (t0) cc_final: 0.3475 (p0) REVERT: E 61 ARG cc_start: 0.6923 (ptm160) cc_final: 0.6371 (ptt-90) REVERT: E 106 LYS cc_start: 0.5744 (mtmt) cc_final: 0.5366 (mttt) REVERT: E 170 ARG cc_start: 0.4958 (tpp-160) cc_final: 0.4706 (mmt180) REVERT: F 89 VAL cc_start: 0.6372 (t) cc_final: 0.5940 (m) REVERT: F 94 GLU cc_start: 0.4666 (mp0) cc_final: 0.4411 (tt0) REVERT: F 125 ARG cc_start: 0.4004 (mmt90) cc_final: 0.3771 (mmt90) REVERT: F 133 ARG cc_start: 0.4310 (mtt-85) cc_final: 0.4010 (mtp85) REVERT: F 150 ARG cc_start: 0.3956 (mtm180) cc_final: 0.3231 (mpp-170) REVERT: G 71 LEU cc_start: 0.5123 (mt) cc_final: 0.4707 (mp) REVERT: G 72 LEU cc_start: 0.4872 (mp) cc_final: 0.4520 (mp) REVERT: G 143 GLN cc_start: 0.6261 (tp-100) cc_final: 0.5980 (tp40) REVERT: G 153 ARG cc_start: 0.4759 (mtt90) cc_final: 0.4455 (ptm-80) REVERT: H 22 LYS cc_start: 0.5719 (mmtp) cc_final: 0.5320 (mttp) REVERT: J 31 GLU cc_start: 0.6378 (tp30) cc_final: 0.5957 (tm-30) REVERT: J 39 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6248 (mmmm) REVERT: J 61 LYS cc_start: 0.6352 (mtmm) cc_final: 0.5600 (mmtt) REVERT: J 85 LYS cc_start: 0.6448 (mttm) cc_final: 0.5904 (mmtm) REVERT: J 90 GLU cc_start: 0.6193 (pt0) cc_final: 0.5269 (tp30) REVERT: J 95 ARG cc_start: 0.5220 (ttm-80) cc_final: 0.4934 (ttp80) REVERT: J 96 ARG cc_start: 0.4651 (mtt180) cc_final: 0.3854 (mmt-90) REVERT: J 99 ARG cc_start: 0.5881 (mmm160) cc_final: 0.5464 (mmp-170) REVERT: J 129 GLU cc_start: 0.5475 (mm-30) cc_final: 0.5142 (tp30) REVERT: J 138 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5756 (mp10) REVERT: K 20 MET cc_start: 0.7430 (ttp) cc_final: 0.7155 (ttm) REVERT: K 53 LYS cc_start: 0.5470 (pttp) cc_final: 0.4869 (tptp) REVERT: K 71 ARG cc_start: 0.6329 (mmt90) cc_final: 0.5798 (mmm160) REVERT: K 88 ASN cc_start: 0.5810 (t0) cc_final: 0.5425 (t0) REVERT: K 98 ARG cc_start: 0.5892 (mmp80) cc_final: 0.5209 (mmm-85) REVERT: K 113 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.4186 (tpt) REVERT: K 114 LYS cc_start: 0.5024 (tptt) cc_final: 0.4686 (tttm) REVERT: K 121 GLU cc_start: 0.6302 (tt0) cc_final: 0.5968 (tt0) REVERT: L 14 LYS cc_start: 0.5496 (tttt) cc_final: 0.5223 (ttpt) REVERT: L 103 ILE cc_start: 0.5847 (mt) cc_final: 0.5643 (pp) REVERT: L 123 ARG cc_start: 0.4484 (mtm-85) cc_final: 0.4170 (mtt90) REVERT: M 5 LYS cc_start: 0.6096 (mtpt) cc_final: 0.5889 (mtpp) REVERT: M 6 ARG cc_start: 0.5374 (ttt-90) cc_final: 0.4779 (mtp85) REVERT: M 30 SER cc_start: 0.6914 (m) cc_final: 0.6459 (p) REVERT: M 36 VAL cc_start: 0.6806 (t) cc_final: 0.6549 (m) REVERT: M 55 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5860 (ttt90) REVERT: M 59 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5723 (mtm180) REVERT: M 115 GLU cc_start: 0.5569 (mm-30) cc_final: 0.5224 (tt0) REVERT: M 118 LYS cc_start: 0.5822 (mmtm) cc_final: 0.5549 (ttmp) REVERT: M 133 LYS cc_start: 0.5435 (ttpp) cc_final: 0.5147 (tttm) REVERT: M 136 MET cc_start: 0.3410 (mtp) cc_final: 0.3160 (mtt) REVERT: N 73 ASN cc_start: 0.6330 (m-40) cc_final: 0.5937 (m-40) REVERT: O 16 ARG cc_start: 0.5774 (mmp80) cc_final: 0.5298 (mmt90) REVERT: O 17 LYS cc_start: 0.5210 (mmtp) cc_final: 0.4921 (tppt) REVERT: O 19 GLN cc_start: 0.5649 (tm-30) cc_final: 0.5403 (tm-30) REVERT: O 91 SER cc_start: 0.6142 (m) cc_final: 0.5519 (p) REVERT: P 6 LYS cc_start: 0.5217 (tptt) cc_final: 0.5008 (mtmt) REVERT: P 7 GLN cc_start: 0.5729 (tt0) cc_final: 0.4955 (mm-40) REVERT: P 13 MET cc_start: 0.5600 (mtp) cc_final: 0.5247 (mmm) REVERT: P 33 VAL cc_start: 0.4661 (t) cc_final: 0.4242 (m) REVERT: P 89 ARG cc_start: 0.5660 (mtm-85) cc_final: 0.5014 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6136 (tpm170) cc_final: 0.5454 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6355 (mtpp) cc_final: 0.6002 (mtmp) REVERT: Q 84 LYS cc_start: 0.5547 (ttpp) cc_final: 0.4940 (mmtm) REVERT: Q 89 GLU cc_start: 0.5512 (mt-10) cc_final: 0.4873 (mm-30) REVERT: R 6 GLN cc_start: 0.5635 (tt0) cc_final: 0.5212 (pt0) REVERT: R 13 ARG cc_start: 0.6443 (ttp80) cc_final: 0.5780 (ttp-170) REVERT: R 34 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4865 (mp0) REVERT: R 60 LYS cc_start: 0.4531 (mttp) cc_final: 0.4240 (mtpt) REVERT: R 86 GLN cc_start: 0.6568 (pt0) cc_final: 0.6233 (pt0) REVERT: S 11 ARG cc_start: 0.5719 (mmt-90) cc_final: 0.5312 (mmm-85) REVERT: S 12 SER cc_start: 0.6710 (t) cc_final: 0.6419 (p) REVERT: T 5 GLU cc_start: 0.4707 (mp0) cc_final: 0.4506 (tt0) REVERT: T 8 LEU cc_start: 0.6286 (mt) cc_final: 0.5945 (mt) REVERT: T 56 GLU cc_start: 0.5458 (tp30) cc_final: 0.5020 (tp30) REVERT: T 69 ARG cc_start: 0.4382 (ptp-170) cc_final: 0.4015 (mtp85) REVERT: T 73 ARG cc_start: 0.3075 (tpt170) cc_final: 0.2738 (ttp-110) REVERT: U 9 ASP cc_start: 0.5114 (m-30) cc_final: 0.4566 (m-30) REVERT: U 26 LYS cc_start: 0.4992 (mmmt) cc_final: 0.4631 (mttp) REVERT: U 46 GLN cc_start: 0.4878 (pt0) cc_final: 0.4664 (mt0) REVERT: V 43 ASP cc_start: 0.5818 (t0) cc_final: 0.5207 (m-30) REVERT: V 48 MET cc_start: 0.5426 (tpt) cc_final: 0.4948 (tpt) REVERT: V 61 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4724 (mt) REVERT: W 29 GLU cc_start: 0.6527 (tt0) cc_final: 0.6159 (mt-10) REVERT: W 39 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.5884 (mtm180) REVERT: W 44 LYS cc_start: 0.6566 (tttt) cc_final: 0.6260 (mtpt) REVERT: W 66 LYS cc_start: 0.6692 (mttt) cc_final: 0.6357 (mtmm) REVERT: W 72 LYS cc_start: 0.5429 (mmmt) cc_final: 0.5057 (mmtm) REVERT: W 78 LYS cc_start: 0.6311 (mttt) cc_final: 0.5807 (mtmm) REVERT: Y 29 ARG cc_start: 0.5077 (mtm-85) cc_final: 0.4589 (ttm-80) REVERT: Z 56 LYS cc_start: 0.5652 (tmtt) cc_final: 0.5117 (ptmm) REVERT: a 37 LYS cc_start: 0.6038 (mtmm) cc_final: 0.5656 (mmmt) REVERT: a 52 ARG cc_start: 0.4928 (ptp90) cc_final: 0.4478 (ttt180) REVERT: b 7 GLU cc_start: 0.5878 (mt-10) cc_final: 0.5437 (tt0) REVERT: b 10 LYS cc_start: 0.4983 (mptt) cc_final: 0.4114 (mmtp) REVERT: b 33 LYS cc_start: 0.5016 (mmtt) cc_final: 0.4695 (mmmm) REVERT: b 35 GLU cc_start: 0.5978 (mt-10) cc_final: 0.5564 (tt0) REVERT: b 44 ARG cc_start: 0.5622 (mtp180) cc_final: 0.4311 (mtp85) REVERT: c 12 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6394 (ttt90) REVERT: c 25 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.5986 (tmmt) REVERT: d 16 LYS cc_start: 0.6261 (tptm) cc_final: 0.5908 (tptt) REVERT: j 21 ARG cc_start: 0.3196 (OUTLIER) cc_final: 0.2426 (ptt180) REVERT: j 47 VAL cc_start: 0.3560 (t) cc_final: 0.3353 (t) REVERT: j 49 MET cc_start: 0.3586 (mtm) cc_final: 0.3275 (mtm) REVERT: j 50 PHE cc_start: 0.3228 (OUTLIER) cc_final: 0.2852 (p90) REVERT: j 64 LYS cc_start: 0.3017 (mtpp) cc_final: 0.2641 (ptpp) REVERT: j 105 LYS cc_start: 0.5191 (tttt) cc_final: 0.4632 (tppp) REVERT: j 169 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5373 (mm-30) REVERT: j 212 LEU cc_start: 0.3296 (tt) cc_final: 0.3006 (tp) REVERT: m 13 GLU cc_start: 0.4983 (pt0) cc_final: 0.4514 (pm20) REVERT: m 26 LYS cc_start: 0.4963 (tptp) cc_final: 0.4751 (ttpt) REVERT: m 30 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6180 (mm) REVERT: m 43 ASN cc_start: 0.4794 (t0) cc_final: 0.4515 (m-40) REVERT: m 45 ARG cc_start: 0.4737 (mmm-85) cc_final: 0.4055 (mmm-85) REVERT: m 55 GLU cc_start: 0.4589 (mm-30) cc_final: 0.3882 (pt0) REVERT: m 61 GLN cc_start: 0.5605 (tt0) cc_final: 0.5185 (tp40) REVERT: m 64 MET cc_start: 0.5512 (mmt) cc_final: 0.5195 (mmt) REVERT: m 65 GLU cc_start: 0.5588 (tt0) cc_final: 0.5200 (tp30) REVERT: m 73 ASN cc_start: 0.5246 (m110) cc_final: 0.4830 (m-40) REVERT: m 93 ARG cc_start: 0.5496 (mpp-170) cc_final: 0.5267 (mtt90) REVERT: m 142 ASP cc_start: 0.4175 (m-30) cc_final: 0.3885 (t0) REVERT: m 156 LYS cc_start: 0.4285 (mtmm) cc_final: 0.4037 (mtmm) REVERT: n 79 ARG cc_start: 0.3709 (ttm-80) cc_final: 0.3452 (ttm170) REVERT: o 9 GLN cc_start: 0.1567 (OUTLIER) cc_final: 0.0987 (mp-120) REVERT: o 74 GLU cc_start: 0.4644 (pt0) cc_final: 0.4093 (tt0) REVERT: o 106 GLU cc_start: 0.4964 (tt0) cc_final: 0.4356 (mm-30) REVERT: o 123 GLU cc_start: 0.4495 (tp30) cc_final: 0.3899 (tm-30) REVERT: o 146 GLU cc_start: 0.4370 (mm-30) cc_final: 0.3980 (tm-30) REVERT: p 40 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5152 (mp) REVERT: p 69 LYS cc_start: 0.3961 (OUTLIER) cc_final: 0.3616 (tppt) REVERT: p 88 ARG cc_start: 0.3930 (mtm180) cc_final: 0.3669 (mtm110) REVERT: q 65 ILE cc_start: 0.4262 (mt) cc_final: 0.4009 (mp) REVERT: q 85 ARG cc_start: 0.4149 (OUTLIER) cc_final: 0.2499 (mpt-90) REVERT: q 105 THR cc_start: 0.4929 (t) cc_final: 0.4597 (t) REVERT: q 106 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.3701 (tpt90) REVERT: q 119 ARG cc_start: 0.4856 (mtm110) cc_final: 0.4318 (mtt180) REVERT: q 124 ARG cc_start: 0.5862 (ttm-80) cc_final: 0.5499 (mtp-110) REVERT: s 52 PHE cc_start: 0.5279 (m-80) cc_final: 0.4918 (m-80) REVERT: s 106 ARG cc_start: 0.3934 (ttt90) cc_final: 0.3324 (tpt-90) REVERT: t 10 LYS cc_start: 0.4632 (ttpt) cc_final: 0.4360 (tttp) REVERT: t 29 GLN cc_start: 0.4652 (mp10) cc_final: 0.3517 (mt0) REVERT: t 31 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.3239 (ttp80) REVERT: t 54 ARG cc_start: 0.3973 (ttp-110) cc_final: 0.3584 (tpp-160) REVERT: t 75 GLN cc_start: 0.1759 (OUTLIER) cc_final: 0.1518 (pt0) REVERT: t 89 ASP cc_start: 0.4316 (OUTLIER) cc_final: 0.4026 (t0) REVERT: t 95 TYR cc_start: 0.5177 (m-80) cc_final: 0.4720 (m-80) REVERT: u 62 LYS cc_start: 0.3234 (mttt) cc_final: 0.2923 (mtpm) REVERT: u 70 ARG cc_start: 0.4192 (mtt-85) cc_final: 0.3955 (mtm-85) REVERT: u 72 GLU cc_start: 0.4294 (mt-10) cc_final: 0.3647 (tp30) REVERT: u 81 MET cc_start: 0.4823 (mtt) cc_final: 0.4328 (mmm) REVERT: u 93 ARG cc_start: 0.4376 (mtp85) cc_final: 0.4154 (mmt90) REVERT: v 21 PHE cc_start: 0.1809 (OUTLIER) cc_final: 0.1339 (m-80) REVERT: v 24 ARG cc_start: 0.3385 (OUTLIER) cc_final: 0.3095 (ttm-80) REVERT: v 47 LYS cc_start: 0.3234 (mmtm) cc_final: 0.2536 (ptpt) REVERT: v 89 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5690 (mmp) REVERT: v 90 ARG cc_start: 0.5803 (mtt90) cc_final: 0.4916 (mtt90) REVERT: v 98 LYS cc_start: 0.5074 (mmmt) cc_final: 0.4333 (mmmm) REVERT: w 38 HIS cc_start: 0.5199 (t70) cc_final: 0.4748 (t70) REVERT: w 58 ARG cc_start: 0.5884 (ttt-90) cc_final: 0.5624 (ttp80) REVERT: w 73 LYS cc_start: 0.3309 (mmmt) cc_final: 0.3025 (mmtp) REVERT: w 84 ARG cc_start: 0.3154 (ttt180) cc_final: 0.2924 (tmt90) REVERT: y 37 PHE cc_start: 0.5955 (m-80) cc_final: 0.5620 (m-80) REVERT: 1 66 MET cc_start: 0.4336 (mtt) cc_final: 0.3788 (mtt) REVERT: 1 81 ARG cc_start: 0.3926 (mpp80) cc_final: 0.3583 (mpp80) REVERT: 2 5 LYS cc_start: 0.3269 (OUTLIER) cc_final: 0.3026 (mmtt) REVERT: 2 16 LYS cc_start: 0.3654 (OUTLIER) cc_final: 0.3398 (ttpp) REVERT: 3 32 VAL cc_start: 0.5206 (t) cc_final: 0.4690 (m) REVERT: 3 34 ARG cc_start: 0.5704 (mmt90) cc_final: 0.5388 (mpt180) REVERT: 3 36 GLU cc_start: 0.6537 (tt0) cc_final: 0.6197 (mt-10) REVERT: 3 39 GLU cc_start: 0.5823 (tm-30) cc_final: 0.5163 (pp20) REVERT: 3 40 LYS cc_start: 0.5926 (tptt) cc_final: 0.5608 (tptm) REVERT: 3 46 LYS cc_start: 0.4869 (ttmt) cc_final: 0.4616 (ttpt) REVERT: e 8 LYS cc_start: 0.6166 (mtpt) cc_final: 0.5709 (ptpt) REVERT: e 15 LYS cc_start: 0.6168 (tttm) cc_final: 0.5506 (tptt) REVERT: e 30 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.4753 (mm-30) outliers start: 156 outliers final: 107 residues processed: 821 average time/residue: 2.3485 time to fit residues: 2721.7110 Evaluate side-chains 838 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 705 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain m residue 159 LYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 LYS Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain v residue 89 MET Chi-restraints excluded: chain w residue 3 LEU Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 17 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 70 LYS Chi-restraints excluded: chain 2 residue 5 LYS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 ARG Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 819 optimal weight: 0.9980 chunk 863 optimal weight: 2.9990 chunk 787 optimal weight: 8.9990 chunk 839 optimal weight: 5.9990 chunk 505 optimal weight: 9.9990 chunk 365 optimal weight: 9.9990 chunk 659 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 758 optimal weight: 9.9990 chunk 794 optimal weight: 10.0000 chunk 836 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN O 38 GLN O 104 GLN b 45 GLN m 78 ASN m 146 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 152207 Z= 0.236 Angle : 0.762 9.016 229001 Z= 0.387 Chirality : 0.041 0.369 29444 Planarity : 0.006 0.081 11367 Dihedral : 23.748 179.447 79419 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 3.70 % Allowed : 17.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 4751 helix: 0.24 (0.13), residues: 1531 sheet: -0.78 (0.16), residues: 930 loop : -0.90 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP j 104 HIS 0.008 0.002 HIS K 29 PHE 0.023 0.003 PHE 1 10 TYR 0.027 0.003 TYR j 213 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 708 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5575 (mttt) cc_final: 0.5048 (mptt) REVERT: C 111 LYS cc_start: 0.5442 (ptmm) cc_final: 0.5197 (ptpp) REVERT: C 125 LYS cc_start: 0.5263 (pttt) cc_final: 0.4919 (ptpt) REVERT: C 133 ARG cc_start: 0.5664 (ptt-90) cc_final: 0.5078 (ttm-80) REVERT: C 163 GLN cc_start: 0.6694 (tt0) cc_final: 0.6104 (mt0) REVERT: C 182 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6577 (ttt180) REVERT: C 183 LYS cc_start: 0.5988 (mttt) cc_final: 0.5635 (mtpt) REVERT: C 199 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6004 (pt0) REVERT: C 201 MET cc_start: 0.7028 (ptt) cc_final: 0.6735 (ptm) REVERT: C 265 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5383 (ptpp) REVERT: C 269 ARG cc_start: 0.6038 (ttp-170) cc_final: 0.5346 (ttt-90) REVERT: D 7 LYS cc_start: 0.6998 (ttpp) cc_final: 0.6715 (ttpp) REVERT: D 17 GLU cc_start: 0.4215 (tt0) cc_final: 0.3899 (mp0) REVERT: D 42 ASN cc_start: 0.4983 (t0) cc_final: 0.4703 (t0) REVERT: D 55 LYS cc_start: 0.5086 (ttmm) cc_final: 0.4734 (ttmt) REVERT: D 70 LYS cc_start: 0.5053 (tttt) cc_final: 0.4759 (tptt) REVERT: D 74 GLU cc_start: 0.4887 (tt0) cc_final: 0.4572 (mp0) REVERT: D 91 THR cc_start: 0.5394 (m) cc_final: 0.4929 (p) REVERT: D 99 GLU cc_start: 0.5168 (tp30) cc_final: 0.4602 (mp0) REVERT: D 105 LYS cc_start: 0.5781 (mttt) cc_final: 0.5533 (mmmm) REVERT: D 128 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6335 (mtp180) REVERT: D 131 ASP cc_start: 0.6862 (m-30) cc_final: 0.6402 (m-30) REVERT: D 183 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.4440 (tp30) REVERT: E 22 ASP cc_start: 0.3897 (t0) cc_final: 0.3464 (p0) REVERT: E 61 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6375 (ptt-90) REVERT: E 106 LYS cc_start: 0.5761 (mtmt) cc_final: 0.5382 (mttt) REVERT: E 170 ARG cc_start: 0.4858 (tpp-160) cc_final: 0.4545 (tpp80) REVERT: F 89 VAL cc_start: 0.6390 (t) cc_final: 0.5956 (m) REVERT: F 94 GLU cc_start: 0.4683 (mp0) cc_final: 0.4444 (tt0) REVERT: F 125 ARG cc_start: 0.3927 (mmt90) cc_final: 0.3686 (mmt90) REVERT: F 133 ARG cc_start: 0.4285 (mtt-85) cc_final: 0.3981 (mtp85) REVERT: F 150 ARG cc_start: 0.3923 (mtm180) cc_final: 0.3175 (mpp-170) REVERT: G 71 LEU cc_start: 0.5114 (mt) cc_final: 0.4688 (mp) REVERT: G 72 LEU cc_start: 0.4862 (mp) cc_final: 0.4621 (mp) REVERT: G 143 GLN cc_start: 0.6241 (tp-100) cc_final: 0.5974 (tp40) REVERT: G 153 ARG cc_start: 0.4755 (mtt90) cc_final: 0.4446 (ptm-80) REVERT: H 22 LYS cc_start: 0.5761 (mmtp) cc_final: 0.5352 (mttp) REVERT: J 31 GLU cc_start: 0.6406 (tp30) cc_final: 0.5973 (tm-30) REVERT: J 39 LYS cc_start: 0.6619 (mtpp) cc_final: 0.6241 (mmmm) REVERT: J 61 LYS cc_start: 0.6356 (mtmm) cc_final: 0.5595 (mmtt) REVERT: J 85 LYS cc_start: 0.6452 (mttm) cc_final: 0.5881 (mmtm) REVERT: J 90 GLU cc_start: 0.6205 (pt0) cc_final: 0.5306 (tp30) REVERT: J 95 ARG cc_start: 0.5218 (ttm-80) cc_final: 0.4944 (ttp80) REVERT: J 96 ARG cc_start: 0.4591 (mtt180) cc_final: 0.3807 (mmt180) REVERT: J 99 ARG cc_start: 0.5880 (mmm160) cc_final: 0.5474 (mmp-170) REVERT: J 129 GLU cc_start: 0.5476 (mm-30) cc_final: 0.5133 (tp30) REVERT: J 138 GLN cc_start: 0.6009 (OUTLIER) cc_final: 0.5731 (mp10) REVERT: K 20 MET cc_start: 0.7414 (ttp) cc_final: 0.7154 (ttm) REVERT: K 53 LYS cc_start: 0.5480 (pttp) cc_final: 0.4872 (tptp) REVERT: K 88 ASN cc_start: 0.5808 (t0) cc_final: 0.5428 (t0) REVERT: K 98 ARG cc_start: 0.5966 (mmp80) cc_final: 0.5247 (mmm-85) REVERT: K 113 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.4178 (tpt) REVERT: K 114 LYS cc_start: 0.5032 (tptt) cc_final: 0.4683 (tttm) REVERT: K 121 GLU cc_start: 0.6290 (tt0) cc_final: 0.5986 (tt0) REVERT: L 14 LYS cc_start: 0.5505 (tttt) cc_final: 0.5233 (ttpt) REVERT: L 103 ILE cc_start: 0.5841 (mt) cc_final: 0.5613 (pp) REVERT: L 123 ARG cc_start: 0.4415 (mtm-85) cc_final: 0.4142 (mtt90) REVERT: M 5 LYS cc_start: 0.6069 (mtpt) cc_final: 0.5863 (mtpp) REVERT: M 6 ARG cc_start: 0.5380 (ttt-90) cc_final: 0.4784 (mtp85) REVERT: M 30 SER cc_start: 0.6931 (m) cc_final: 0.6491 (p) REVERT: M 36 VAL cc_start: 0.6802 (t) cc_final: 0.6557 (m) REVERT: M 55 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5872 (ttt90) REVERT: M 59 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5712 (mtm180) REVERT: M 115 GLU cc_start: 0.5558 (mm-30) cc_final: 0.5205 (tt0) REVERT: M 118 LYS cc_start: 0.5805 (mmtm) cc_final: 0.5541 (ttmp) REVERT: M 127 LYS cc_start: 0.6034 (ttmt) cc_final: 0.5414 (tptp) REVERT: M 136 MET cc_start: 0.3426 (mtp) cc_final: 0.2244 (mpt) REVERT: N 73 ASN cc_start: 0.6269 (m-40) cc_final: 0.5892 (m-40) REVERT: O 16 ARG cc_start: 0.5777 (mmp80) cc_final: 0.5295 (mmt90) REVERT: O 17 LYS cc_start: 0.5214 (mmtp) cc_final: 0.4923 (tppt) REVERT: O 19 GLN cc_start: 0.5651 (tm-30) cc_final: 0.5406 (tm-30) REVERT: O 91 SER cc_start: 0.6094 (m) cc_final: 0.5484 (p) REVERT: P 6 LYS cc_start: 0.5230 (tptt) cc_final: 0.5005 (mtmt) REVERT: P 7 GLN cc_start: 0.5722 (tt0) cc_final: 0.4948 (mm-40) REVERT: P 13 MET cc_start: 0.5600 (mtp) cc_final: 0.5235 (mmm) REVERT: P 33 VAL cc_start: 0.4688 (t) cc_final: 0.4270 (m) REVERT: P 89 ARG cc_start: 0.5666 (mtm-85) cc_final: 0.5035 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6140 (tpm170) cc_final: 0.5453 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6358 (mtpp) cc_final: 0.6007 (mtmp) REVERT: Q 84 LYS cc_start: 0.5551 (ttpp) cc_final: 0.4946 (mmtm) REVERT: Q 89 GLU cc_start: 0.5510 (mt-10) cc_final: 0.4871 (mm-30) REVERT: R 6 GLN cc_start: 0.5631 (tt0) cc_final: 0.5208 (pt0) REVERT: R 13 ARG cc_start: 0.6439 (ttp80) cc_final: 0.5779 (ttp-170) REVERT: R 34 GLU cc_start: 0.5201 (mt-10) cc_final: 0.4825 (mp0) REVERT: R 60 LYS cc_start: 0.4481 (mttp) cc_final: 0.4189 (mtpt) REVERT: R 86 GLN cc_start: 0.6565 (pt0) cc_final: 0.6230 (pt0) REVERT: S 11 ARG cc_start: 0.5709 (mmt-90) cc_final: 0.5310 (mmm-85) REVERT: S 12 SER cc_start: 0.6709 (t) cc_final: 0.6429 (p) REVERT: T 5 GLU cc_start: 0.4709 (mp0) cc_final: 0.4507 (tt0) REVERT: T 8 LEU cc_start: 0.6255 (mt) cc_final: 0.5897 (mt) REVERT: T 56 GLU cc_start: 0.5457 (tp30) cc_final: 0.5019 (tp30) REVERT: T 69 ARG cc_start: 0.4384 (ptp-170) cc_final: 0.4017 (mtp85) REVERT: T 73 ARG cc_start: 0.3102 (tpt170) cc_final: 0.2738 (ttp-110) REVERT: U 9 ASP cc_start: 0.5117 (m-30) cc_final: 0.4569 (m-30) REVERT: U 26 LYS cc_start: 0.4992 (mmmt) cc_final: 0.4630 (mttp) REVERT: V 43 ASP cc_start: 0.5805 (t0) cc_final: 0.5190 (m-30) REVERT: V 48 MET cc_start: 0.5430 (tpt) cc_final: 0.4911 (tpt) REVERT: V 61 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4732 (mt) REVERT: V 65 VAL cc_start: 0.5139 (OUTLIER) cc_final: 0.4837 (p) REVERT: W 29 GLU cc_start: 0.6520 (tt0) cc_final: 0.6177 (mt-10) REVERT: W 39 ARG cc_start: 0.6462 (mtt-85) cc_final: 0.5882 (mtm180) REVERT: W 44 LYS cc_start: 0.6565 (tttt) cc_final: 0.6265 (mtpt) REVERT: W 66 LYS cc_start: 0.6696 (mttt) cc_final: 0.6361 (mtmm) REVERT: W 72 LYS cc_start: 0.5426 (mmmt) cc_final: 0.5057 (mmtm) REVERT: W 78 LYS cc_start: 0.6225 (mttt) cc_final: 0.5723 (mtmm) REVERT: Y 14 LEU cc_start: 0.4973 (mt) cc_final: 0.4734 (mp) REVERT: Y 29 ARG cc_start: 0.5075 (mtm-85) cc_final: 0.4617 (ttm-80) REVERT: Z 56 LYS cc_start: 0.5654 (tmtt) cc_final: 0.5123 (ptmm) REVERT: a 37 LYS cc_start: 0.6032 (mtmm) cc_final: 0.5639 (mmmt) REVERT: a 52 ARG cc_start: 0.4966 (ptp90) cc_final: 0.4497 (ttt180) REVERT: b 7 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5451 (tt0) REVERT: b 10 LYS cc_start: 0.4938 (mptt) cc_final: 0.4073 (mmtp) REVERT: b 33 LYS cc_start: 0.5005 (mmtt) cc_final: 0.4658 (mmmm) REVERT: b 35 GLU cc_start: 0.5976 (mt-10) cc_final: 0.5560 (tt0) REVERT: b 44 ARG cc_start: 0.5641 (mtp180) cc_final: 0.4320 (mtp85) REVERT: c 12 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6391 (ttt90) REVERT: c 25 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.5990 (tmmt) REVERT: d 16 LYS cc_start: 0.6266 (tptm) cc_final: 0.5912 (tptt) REVERT: j 21 ARG cc_start: 0.3208 (OUTLIER) cc_final: 0.2435 (ptt180) REVERT: j 47 VAL cc_start: 0.3561 (t) cc_final: 0.3356 (t) REVERT: j 49 MET cc_start: 0.3556 (mtm) cc_final: 0.3248 (mtm) REVERT: j 50 PHE cc_start: 0.3257 (OUTLIER) cc_final: 0.2882 (p90) REVERT: j 64 LYS cc_start: 0.3018 (mtpp) cc_final: 0.2642 (ptpp) REVERT: j 105 LYS cc_start: 0.5168 (tttt) cc_final: 0.4589 (tppp) REVERT: j 169 GLU cc_start: 0.5610 (mm-30) cc_final: 0.5389 (mm-30) REVERT: j 212 LEU cc_start: 0.3154 (tt) cc_final: 0.2855 (tp) REVERT: m 13 GLU cc_start: 0.4987 (pt0) cc_final: 0.4514 (pm20) REVERT: m 26 LYS cc_start: 0.4991 (tptp) cc_final: 0.4765 (ttpt) REVERT: m 30 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6197 (mm) REVERT: m 43 ASN cc_start: 0.4787 (t0) cc_final: 0.4507 (m-40) REVERT: m 45 ARG cc_start: 0.4739 (mmm-85) cc_final: 0.4050 (mmm-85) REVERT: m 55 GLU cc_start: 0.4588 (mm-30) cc_final: 0.3880 (pt0) REVERT: m 61 GLN cc_start: 0.5632 (tt0) cc_final: 0.5208 (tp40) REVERT: m 64 MET cc_start: 0.5534 (mmt) cc_final: 0.5225 (mmt) REVERT: m 65 GLU cc_start: 0.5588 (tt0) cc_final: 0.5196 (tp30) REVERT: m 73 ASN cc_start: 0.5211 (m110) cc_final: 0.4799 (m-40) REVERT: m 93 ARG cc_start: 0.5480 (mpp-170) cc_final: 0.5248 (mtt90) REVERT: m 142 ASP cc_start: 0.4175 (m-30) cc_final: 0.3895 (t0) REVERT: m 156 LYS cc_start: 0.4274 (mtmm) cc_final: 0.4023 (mtmm) REVERT: n 79 ARG cc_start: 0.3784 (ttm-80) cc_final: 0.3528 (ttm170) REVERT: o 74 GLU cc_start: 0.4639 (pt0) cc_final: 0.4091 (tt0) REVERT: o 106 GLU cc_start: 0.4942 (tt0) cc_final: 0.4337 (mm-30) REVERT: o 123 GLU cc_start: 0.4465 (tp30) cc_final: 0.3866 (tm-30) REVERT: o 146 GLU cc_start: 0.4384 (mm-30) cc_final: 0.3985 (tm-30) REVERT: p 40 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.5149 (mp) REVERT: p 69 LYS cc_start: 0.3946 (OUTLIER) cc_final: 0.3598 (tppt) REVERT: p 88 ARG cc_start: 0.3943 (mtm180) cc_final: 0.3647 (mtm110) REVERT: p 89 LYS cc_start: 0.3909 (ttpt) cc_final: 0.3696 (ttpp) REVERT: q 65 ILE cc_start: 0.4280 (mt) cc_final: 0.4023 (mp) REVERT: q 85 ARG cc_start: 0.4174 (OUTLIER) cc_final: 0.2513 (mpt-90) REVERT: q 106 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.3672 (tpt90) REVERT: q 119 ARG cc_start: 0.4882 (mtm110) cc_final: 0.4299 (mtt180) REVERT: q 124 ARG cc_start: 0.5810 (ttm-80) cc_final: 0.5450 (mtp-110) REVERT: s 106 ARG cc_start: 0.3927 (ttt90) cc_final: 0.3316 (tpt-90) REVERT: t 10 LYS cc_start: 0.4640 (ttpt) cc_final: 0.4365 (tttp) REVERT: t 29 GLN cc_start: 0.4703 (mp10) cc_final: 0.3563 (mt0) REVERT: t 31 ARG cc_start: 0.4008 (OUTLIER) cc_final: 0.3230 (ttp80) REVERT: t 54 ARG cc_start: 0.3997 (ttp-110) cc_final: 0.3610 (tpp-160) REVERT: t 75 GLN cc_start: 0.1852 (OUTLIER) cc_final: 0.1581 (pt0) REVERT: t 89 ASP cc_start: 0.4324 (OUTLIER) cc_final: 0.4022 (t0) REVERT: t 95 TYR cc_start: 0.5161 (m-80) cc_final: 0.4694 (m-80) REVERT: u 29 ARG cc_start: 0.3988 (mmt180) cc_final: 0.3513 (tpp-160) REVERT: u 62 LYS cc_start: 0.3344 (mttt) cc_final: 0.3074 (mtpm) REVERT: u 70 ARG cc_start: 0.4197 (mtt-85) cc_final: 0.3961 (mtm-85) REVERT: u 72 GLU cc_start: 0.4412 (mt-10) cc_final: 0.3723 (tp30) REVERT: u 81 MET cc_start: 0.4819 (mtt) cc_final: 0.4380 (mmm) REVERT: u 93 ARG cc_start: 0.4384 (mtp85) cc_final: 0.4164 (mmt90) REVERT: v 21 PHE cc_start: 0.1775 (OUTLIER) cc_final: 0.1319 (m-80) REVERT: v 24 ARG cc_start: 0.3467 (OUTLIER) cc_final: 0.3157 (ttm-80) REVERT: v 47 LYS cc_start: 0.3276 (mmtm) cc_final: 0.2568 (ptpt) REVERT: v 89 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5598 (mmp) REVERT: v 90 ARG cc_start: 0.5855 (mtt90) cc_final: 0.4970 (mtt90) REVERT: v 98 LYS cc_start: 0.5077 (mmmt) cc_final: 0.4336 (mmmm) REVERT: w 38 HIS cc_start: 0.5201 (t70) cc_final: 0.4751 (t70) REVERT: w 58 ARG cc_start: 0.5868 (ttt-90) cc_final: 0.5620 (ttp80) REVERT: w 73 LYS cc_start: 0.3310 (mmmt) cc_final: 0.3025 (mmtp) REVERT: w 84 ARG cc_start: 0.3201 (ttt180) cc_final: 0.2956 (ttt180) REVERT: y 4 LYS cc_start: 0.0839 (OUTLIER) cc_final: 0.0512 (tmtt) REVERT: y 37 PHE cc_start: 0.5940 (m-80) cc_final: 0.5623 (m-80) REVERT: 1 37 ARG cc_start: 0.4993 (ptp90) cc_final: 0.4446 (ptt-90) REVERT: 1 66 MET cc_start: 0.4348 (mtt) cc_final: 0.3710 (mtt) REVERT: 1 81 ARG cc_start: 0.3927 (mpp80) cc_final: 0.3578 (mpp80) REVERT: 2 16 LYS cc_start: 0.3674 (OUTLIER) cc_final: 0.3416 (ttpp) REVERT: 3 32 VAL cc_start: 0.5202 (t) cc_final: 0.4688 (m) REVERT: 3 36 GLU cc_start: 0.6561 (tt0) cc_final: 0.6212 (mt-10) REVERT: 3 39 GLU cc_start: 0.5823 (tm-30) cc_final: 0.5146 (pp20) REVERT: 3 40 LYS cc_start: 0.5916 (tptt) cc_final: 0.5598 (tptm) REVERT: 3 46 LYS cc_start: 0.4872 (ttmt) cc_final: 0.4618 (ttpt) REVERT: e 8 LYS cc_start: 0.6202 (mtpt) cc_final: 0.5757 (ptpt) REVERT: e 15 LYS cc_start: 0.6170 (tttm) cc_final: 0.5519 (tptt) REVERT: e 30 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4751 (mm-30) outliers start: 146 outliers final: 109 residues processed: 800 average time/residue: 2.3650 time to fit residues: 2665.1845 Evaluate side-chains 842 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 707 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 78 GLU Chi-restraints excluded: chain j residue 161 LEU Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain m residue 159 LYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 LYS Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain v residue 89 MET Chi-restraints excluded: chain w residue 3 LEU Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 70 LYS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 ARG Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 551 optimal weight: 9.9990 chunk 888 optimal weight: 6.9990 chunk 542 optimal weight: 0.8980 chunk 421 optimal weight: 0.6980 chunk 617 optimal weight: 30.0000 chunk 931 optimal weight: 20.0000 chunk 857 optimal weight: 6.9990 chunk 741 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 572 optimal weight: 5.9990 chunk 454 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN O 104 GLN U 46 GLN b 45 GLN m 78 ASN m 146 ASN ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 GLN v 43 ASN 2 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 152207 Z= 0.194 Angle : 0.685 9.923 229001 Z= 0.353 Chirality : 0.039 0.307 29444 Planarity : 0.005 0.070 11367 Dihedral : 23.682 179.631 79419 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 3.64 % Allowed : 17.84 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4751 helix: 0.39 (0.13), residues: 1553 sheet: -0.71 (0.16), residues: 928 loop : -0.85 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP j 104 HIS 0.007 0.002 HIS E 165 PHE 0.021 0.002 PHE 3 37 TYR 0.022 0.002 TYR j 213 ARG 0.007 0.001 ARG Z 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 708 time to evaluate : 5.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.5548 (mttt) cc_final: 0.5030 (mptt) REVERT: C 13 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.5299 (mmm160) REVERT: C 111 LYS cc_start: 0.5443 (ptmm) cc_final: 0.5200 (ptpp) REVERT: C 125 LYS cc_start: 0.5275 (pttt) cc_final: 0.4925 (ptpt) REVERT: C 133 ARG cc_start: 0.5752 (ptt-90) cc_final: 0.5147 (ttm-80) REVERT: C 163 GLN cc_start: 0.6680 (tt0) cc_final: 0.6081 (mt0) REVERT: C 182 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6580 (ttt180) REVERT: C 183 LYS cc_start: 0.6049 (mttt) cc_final: 0.5651 (mtpt) REVERT: C 199 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6001 (pt0) REVERT: C 201 MET cc_start: 0.7012 (ptt) cc_final: 0.6719 (ptm) REVERT: C 269 ARG cc_start: 0.6070 (ttp-170) cc_final: 0.5369 (ttt-90) REVERT: D 7 LYS cc_start: 0.7012 (ttpp) cc_final: 0.6729 (ttpp) REVERT: D 17 GLU cc_start: 0.4163 (tt0) cc_final: 0.3901 (mp0) REVERT: D 42 ASN cc_start: 0.4978 (t0) cc_final: 0.4704 (t0) REVERT: D 55 LYS cc_start: 0.5098 (ttmm) cc_final: 0.4798 (ttmt) REVERT: D 70 LYS cc_start: 0.5054 (tttt) cc_final: 0.4756 (tptt) REVERT: D 99 GLU cc_start: 0.5204 (tp30) cc_final: 0.4632 (mp0) REVERT: D 105 LYS cc_start: 0.6030 (mttt) cc_final: 0.5608 (mmmt) REVERT: D 128 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6325 (mtp180) REVERT: D 131 ASP cc_start: 0.6848 (m-30) cc_final: 0.6389 (m-30) REVERT: D 183 GLU cc_start: 0.4619 (OUTLIER) cc_final: 0.4408 (tp30) REVERT: E 22 ASP cc_start: 0.3876 (t0) cc_final: 0.3430 (p0) REVERT: E 61 ARG cc_start: 0.6909 (ptm160) cc_final: 0.6372 (ptt-90) REVERT: E 106 LYS cc_start: 0.5753 (mtmt) cc_final: 0.5371 (mttt) REVERT: E 170 ARG cc_start: 0.4860 (tpp-160) cc_final: 0.4586 (tpp80) REVERT: F 38 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4788 (mtp) REVERT: F 89 VAL cc_start: 0.6391 (t) cc_final: 0.5942 (m) REVERT: F 94 GLU cc_start: 0.4638 (mp0) cc_final: 0.4414 (tt0) REVERT: F 125 ARG cc_start: 0.3940 (mmt90) cc_final: 0.3694 (mmt90) REVERT: F 133 ARG cc_start: 0.4315 (mtt-85) cc_final: 0.4019 (mtp85) REVERT: F 150 ARG cc_start: 0.3954 (mtm180) cc_final: 0.3203 (mpp-170) REVERT: G 71 LEU cc_start: 0.5134 (mt) cc_final: 0.4720 (mp) REVERT: G 72 LEU cc_start: 0.4860 (mp) cc_final: 0.4606 (mp) REVERT: G 143 GLN cc_start: 0.6217 (tp-100) cc_final: 0.5943 (tp40) REVERT: G 153 ARG cc_start: 0.4750 (mtt90) cc_final: 0.4441 (ptm-80) REVERT: H 22 LYS cc_start: 0.5737 (mmtp) cc_final: 0.5241 (mttp) REVERT: J 31 GLU cc_start: 0.6314 (tp30) cc_final: 0.6001 (tm-30) REVERT: J 39 LYS cc_start: 0.6612 (mtpp) cc_final: 0.6235 (mmmm) REVERT: J 61 LYS cc_start: 0.6357 (mtmm) cc_final: 0.5596 (mmtt) REVERT: J 85 LYS cc_start: 0.6452 (mttm) cc_final: 0.5880 (mmtm) REVERT: J 90 GLU cc_start: 0.6201 (pt0) cc_final: 0.5304 (tp30) REVERT: J 95 ARG cc_start: 0.5233 (ttm-80) cc_final: 0.5019 (ttp-170) REVERT: J 96 ARG cc_start: 0.4591 (mtt180) cc_final: 0.3815 (mmt180) REVERT: J 99 ARG cc_start: 0.5879 (mmm160) cc_final: 0.5466 (mmp-170) REVERT: J 129 GLU cc_start: 0.5507 (mm-30) cc_final: 0.5159 (tp30) REVERT: J 138 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.5698 (mp10) REVERT: K 20 MET cc_start: 0.7425 (ttp) cc_final: 0.7176 (ttm) REVERT: K 53 LYS cc_start: 0.5547 (pttp) cc_final: 0.4927 (tptp) REVERT: K 88 ASN cc_start: 0.5808 (t0) cc_final: 0.5428 (t0) REVERT: K 98 ARG cc_start: 0.5920 (mmp80) cc_final: 0.5209 (mmm-85) REVERT: K 113 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.4234 (tpt) REVERT: K 114 LYS cc_start: 0.5036 (tptt) cc_final: 0.4683 (tttm) REVERT: K 121 GLU cc_start: 0.6276 (tt0) cc_final: 0.5983 (tt0) REVERT: L 14 LYS cc_start: 0.5478 (tttt) cc_final: 0.5192 (ttpt) REVERT: L 17 LYS cc_start: 0.6681 (mttt) cc_final: 0.6432 (mttm) REVERT: L 103 ILE cc_start: 0.5829 (mt) cc_final: 0.5613 (pp) REVERT: L 123 ARG cc_start: 0.4415 (mtm-85) cc_final: 0.4113 (mtt90) REVERT: M 5 LYS cc_start: 0.6054 (mtpt) cc_final: 0.5847 (mtpt) REVERT: M 6 ARG cc_start: 0.5403 (ttt-90) cc_final: 0.4817 (mtp85) REVERT: M 30 SER cc_start: 0.6915 (m) cc_final: 0.6523 (p) REVERT: M 36 VAL cc_start: 0.6784 (t) cc_final: 0.6545 (m) REVERT: M 55 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5903 (ttt90) REVERT: M 59 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5710 (mtm180) REVERT: M 115 GLU cc_start: 0.5523 (mm-30) cc_final: 0.5164 (tt0) REVERT: M 118 LYS cc_start: 0.5808 (mmtm) cc_final: 0.5546 (ttmp) REVERT: M 127 LYS cc_start: 0.6051 (ttmt) cc_final: 0.5438 (tptp) REVERT: M 136 MET cc_start: 0.3477 (mtp) cc_final: 0.2250 (mpt) REVERT: N 73 ASN cc_start: 0.6296 (m-40) cc_final: 0.5917 (m-40) REVERT: O 16 ARG cc_start: 0.5724 (mmp80) cc_final: 0.5029 (mmt90) REVERT: O 17 LYS cc_start: 0.5204 (mmtp) cc_final: 0.4923 (tppt) REVERT: O 19 GLN cc_start: 0.5606 (tm-30) cc_final: 0.5378 (tm-30) REVERT: O 91 SER cc_start: 0.6089 (m) cc_final: 0.5473 (p) REVERT: P 6 LYS cc_start: 0.5198 (tptt) cc_final: 0.4992 (mtmt) REVERT: P 7 GLN cc_start: 0.5729 (tt0) cc_final: 0.4958 (mm-40) REVERT: P 13 MET cc_start: 0.5601 (mtp) cc_final: 0.5273 (mmm) REVERT: P 33 VAL cc_start: 0.4711 (t) cc_final: 0.4288 (m) REVERT: P 89 ARG cc_start: 0.5656 (mtm-85) cc_final: 0.5035 (mtt-85) REVERT: Q 11 ARG cc_start: 0.6150 (tpm170) cc_final: 0.5456 (ttp-110) REVERT: Q 78 LYS cc_start: 0.6339 (mtpp) cc_final: 0.5993 (mtmp) REVERT: Q 84 LYS cc_start: 0.5541 (ttpp) cc_final: 0.4950 (mmtm) REVERT: Q 89 GLU cc_start: 0.5528 (mt-10) cc_final: 0.4884 (mm-30) REVERT: R 6 GLN cc_start: 0.5622 (tt0) cc_final: 0.5235 (pt0) REVERT: R 13 ARG cc_start: 0.6442 (ttp80) cc_final: 0.5803 (ttp-170) REVERT: R 34 GLU cc_start: 0.5199 (mt-10) cc_final: 0.4764 (mp0) REVERT: R 60 LYS cc_start: 0.4522 (mttp) cc_final: 0.4209 (mtpt) REVERT: R 86 GLN cc_start: 0.6587 (pt0) cc_final: 0.6251 (pt0) REVERT: S 11 ARG cc_start: 0.5758 (mmt-90) cc_final: 0.5277 (mmm-85) REVERT: S 12 SER cc_start: 0.6720 (t) cc_final: 0.6432 (p) REVERT: S 68 ASP cc_start: 0.5391 (OUTLIER) cc_final: 0.4835 (p0) REVERT: T 5 GLU cc_start: 0.4670 (mp0) cc_final: 0.4459 (tt0) REVERT: T 8 LEU cc_start: 0.6286 (mt) cc_final: 0.5939 (mt) REVERT: T 56 GLU cc_start: 0.5473 (tp30) cc_final: 0.5006 (tp30) REVERT: T 69 ARG cc_start: 0.4419 (ptp-170) cc_final: 0.4043 (mtp85) REVERT: T 73 ARG cc_start: 0.3198 (tpt170) cc_final: 0.2839 (ttp-110) REVERT: U 9 ASP cc_start: 0.5112 (m-30) cc_final: 0.4578 (m-30) REVERT: U 26 LYS cc_start: 0.4938 (mmmt) cc_final: 0.4600 (mttp) REVERT: V 43 ASP cc_start: 0.5821 (t0) cc_final: 0.5199 (m-30) REVERT: V 48 MET cc_start: 0.5390 (tpt) cc_final: 0.4858 (tpt) REVERT: V 61 LEU cc_start: 0.5071 (OUTLIER) cc_final: 0.4755 (mt) REVERT: V 65 VAL cc_start: 0.5246 (OUTLIER) cc_final: 0.4941 (p) REVERT: W 29 GLU cc_start: 0.6575 (tt0) cc_final: 0.6215 (mt-10) REVERT: W 39 ARG cc_start: 0.6457 (mtt-85) cc_final: 0.5877 (mtm180) REVERT: W 44 LYS cc_start: 0.6541 (tttt) cc_final: 0.6246 (mtpt) REVERT: W 66 LYS cc_start: 0.6723 (mttt) cc_final: 0.6389 (mtmm) REVERT: W 72 LYS cc_start: 0.5347 (mmmt) cc_final: 0.4998 (mmtm) REVERT: W 78 LYS cc_start: 0.6286 (mttt) cc_final: 0.5797 (mtmm) REVERT: Y 14 LEU cc_start: 0.4885 (mt) cc_final: 0.4663 (mp) REVERT: Y 29 ARG cc_start: 0.5077 (mtm-85) cc_final: 0.4536 (ttm-80) REVERT: Z 56 LYS cc_start: 0.5675 (tmtt) cc_final: 0.5137 (ptmm) REVERT: a 37 LYS cc_start: 0.6099 (mtmm) cc_final: 0.5729 (mmmt) REVERT: a 52 ARG cc_start: 0.4952 (ptp90) cc_final: 0.4532 (ttt180) REVERT: b 7 GLU cc_start: 0.5920 (mt-10) cc_final: 0.5464 (pt0) REVERT: b 10 LYS cc_start: 0.4927 (mptt) cc_final: 0.4531 (ptpt) REVERT: b 33 LYS cc_start: 0.4957 (mmtt) cc_final: 0.4619 (mmmm) REVERT: b 35 GLU cc_start: 0.5966 (mt-10) cc_final: 0.5556 (tt0) REVERT: b 44 ARG cc_start: 0.5572 (mtp180) cc_final: 0.4274 (mtp85) REVERT: c 12 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6399 (ttt90) REVERT: c 25 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.5991 (tmmt) REVERT: d 16 LYS cc_start: 0.6417 (tptm) cc_final: 0.6054 (tptt) REVERT: j 21 ARG cc_start: 0.3114 (OUTLIER) cc_final: 0.2364 (pmm-80) REVERT: j 49 MET cc_start: 0.3550 (mtm) cc_final: 0.3231 (mtm) REVERT: j 50 PHE cc_start: 0.3258 (OUTLIER) cc_final: 0.2884 (p90) REVERT: j 64 LYS cc_start: 0.2855 (mtpp) cc_final: 0.2506 (ptpp) REVERT: j 105 LYS cc_start: 0.5196 (tttt) cc_final: 0.4598 (tppp) REVERT: j 109 GLN cc_start: 0.4256 (mm-40) cc_final: 0.3722 (mt0) REVERT: j 169 GLU cc_start: 0.5679 (mm-30) cc_final: 0.5445 (mm-30) REVERT: j 212 LEU cc_start: 0.3092 (tt) cc_final: 0.2779 (tp) REVERT: m 13 GLU cc_start: 0.4986 (pt0) cc_final: 0.4510 (pm20) REVERT: m 26 LYS cc_start: 0.4972 (tptp) cc_final: 0.4731 (tptt) REVERT: m 30 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6210 (mm) REVERT: m 43 ASN cc_start: 0.4788 (t0) cc_final: 0.4507 (m-40) REVERT: m 45 ARG cc_start: 0.4802 (mmm-85) cc_final: 0.4093 (mmm-85) REVERT: m 55 GLU cc_start: 0.4600 (mm-30) cc_final: 0.3889 (pt0) REVERT: m 61 GLN cc_start: 0.5669 (tt0) cc_final: 0.5252 (tp40) REVERT: m 64 MET cc_start: 0.5419 (mmt) cc_final: 0.5131 (mmt) REVERT: m 65 GLU cc_start: 0.5572 (tt0) cc_final: 0.5194 (tp30) REVERT: m 73 ASN cc_start: 0.5337 (m110) cc_final: 0.4971 (m-40) REVERT: m 93 ARG cc_start: 0.5474 (mpp-170) cc_final: 0.5237 (mtt90) REVERT: m 142 ASP cc_start: 0.4085 (m-30) cc_final: 0.3802 (t0) REVERT: m 156 LYS cc_start: 0.4191 (mtmm) cc_final: 0.3965 (mtmm) REVERT: n 79 ARG cc_start: 0.3807 (ttm-80) cc_final: 0.3562 (ttm170) REVERT: o 74 GLU cc_start: 0.4636 (pt0) cc_final: 0.4081 (tt0) REVERT: o 106 GLU cc_start: 0.4921 (tt0) cc_final: 0.4315 (mm-30) REVERT: o 123 GLU cc_start: 0.4448 (tp30) cc_final: 0.3880 (tm-30) REVERT: o 146 GLU cc_start: 0.4417 (mm-30) cc_final: 0.3995 (tm-30) REVERT: p 40 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.5012 (mp) REVERT: p 69 LYS cc_start: 0.3956 (OUTLIER) cc_final: 0.3613 (tppt) REVERT: p 88 ARG cc_start: 0.3878 (mtm180) cc_final: 0.3573 (mtm110) REVERT: q 65 ILE cc_start: 0.4360 (mt) cc_final: 0.4136 (mp) REVERT: q 85 ARG cc_start: 0.4175 (OUTLIER) cc_final: 0.2473 (mpt-90) REVERT: q 106 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.3745 (tpt90) REVERT: q 119 ARG cc_start: 0.4851 (mtm110) cc_final: 0.4273 (mtt180) REVERT: q 124 ARG cc_start: 0.5806 (ttm-80) cc_final: 0.5245 (mtp-110) REVERT: s 106 ARG cc_start: 0.4020 (ttt90) cc_final: 0.3391 (tpt-90) REVERT: t 29 GLN cc_start: 0.4891 (mp10) cc_final: 0.3820 (mt0) REVERT: t 31 ARG cc_start: 0.3996 (OUTLIER) cc_final: 0.3224 (ttp80) REVERT: t 54 ARG cc_start: 0.3956 (ttp-110) cc_final: 0.3575 (tpp-160) REVERT: t 75 GLN cc_start: 0.1698 (OUTLIER) cc_final: 0.1427 (pt0) REVERT: t 89 ASP cc_start: 0.4328 (OUTLIER) cc_final: 0.4018 (t0) REVERT: t 95 TYR cc_start: 0.5144 (m-80) cc_final: 0.4601 (m-80) REVERT: u 29 ARG cc_start: 0.3987 (mmt180) cc_final: 0.3503 (tmt-80) REVERT: u 62 LYS cc_start: 0.3248 (mttt) cc_final: 0.2974 (mtpm) REVERT: u 70 ARG cc_start: 0.4278 (mtt-85) cc_final: 0.4022 (mtm-85) REVERT: u 72 GLU cc_start: 0.4380 (mt-10) cc_final: 0.3683 (tp30) REVERT: u 81 MET cc_start: 0.4748 (mtt) cc_final: 0.4357 (mmm) REVERT: u 93 ARG cc_start: 0.4376 (mtp85) cc_final: 0.4160 (mmt90) REVERT: v 21 PHE cc_start: 0.1827 (OUTLIER) cc_final: 0.1356 (m-80) REVERT: v 24 ARG cc_start: 0.3482 (OUTLIER) cc_final: 0.3157 (ttm-80) REVERT: v 47 LYS cc_start: 0.3306 (mmtm) cc_final: 0.2603 (ptpt) REVERT: v 89 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5572 (mmp) REVERT: v 90 ARG cc_start: 0.5799 (mtt90) cc_final: 0.4915 (mtt90) REVERT: v 98 LYS cc_start: 0.4998 (mmmt) cc_final: 0.4261 (mmmm) REVERT: w 38 HIS cc_start: 0.5228 (t70) cc_final: 0.4783 (t70) REVERT: w 58 ARG cc_start: 0.5863 (ttt-90) cc_final: 0.5622 (ttp80) REVERT: w 73 LYS cc_start: 0.3274 (mmmt) cc_final: 0.3007 (mmtp) REVERT: w 84 ARG cc_start: 0.3206 (ttt180) cc_final: 0.2910 (tmt90) REVERT: 1 37 ARG cc_start: 0.4937 (ptp90) cc_final: 0.4413 (ptt-90) REVERT: 1 66 MET cc_start: 0.4348 (mtt) cc_final: 0.3705 (mtt) REVERT: 1 81 ARG cc_start: 0.3895 (mpp80) cc_final: 0.3546 (mpp80) REVERT: 2 5 LYS cc_start: 0.3224 (OUTLIER) cc_final: 0.2994 (mmtt) REVERT: 2 16 LYS cc_start: 0.3579 (OUTLIER) cc_final: 0.3361 (ttpp) REVERT: 3 32 VAL cc_start: 0.5144 (t) cc_final: 0.4641 (m) REVERT: 3 36 GLU cc_start: 0.6702 (tt0) cc_final: 0.6274 (mm-30) REVERT: 3 39 GLU cc_start: 0.5679 (tm-30) cc_final: 0.4986 (pp20) REVERT: 3 40 LYS cc_start: 0.5841 (tptt) cc_final: 0.5596 (tptm) REVERT: 3 46 LYS cc_start: 0.4920 (ttmt) cc_final: 0.4658 (ttpt) REVERT: e 8 LYS cc_start: 0.6110 (mtpt) cc_final: 0.5596 (pttt) REVERT: e 15 LYS cc_start: 0.6203 (tttm) cc_final: 0.5523 (tptt) REVERT: e 30 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.4791 (mm-30) outliers start: 144 outliers final: 104 residues processed: 800 average time/residue: 2.2564 time to fit residues: 2535.0708 Evaluate side-chains 828 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 696 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 37 GLU Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain j residue 21 ARG Chi-restraints excluded: chain j residue 50 PHE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 78 GLU Chi-restraints excluded: chain j residue 108 ARG Chi-restraints excluded: chain j residue 161 LEU Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain j residue 207 ILE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 85 VAL Chi-restraints excluded: chain m residue 159 LYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 64 VAL Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 9 GLN Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 138 ARG Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain p residue 50 LYS Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 113 ASP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 84 THR Chi-restraints excluded: chain q residue 85 ARG Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 116 ILE Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 31 ARG Chi-restraints excluded: chain t residue 36 ARG Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 52 VAL Chi-restraints excluded: chain t residue 75 GLN Chi-restraints excluded: chain t residue 89 ASP Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 21 PHE Chi-restraints excluded: chain v residue 24 ARG Chi-restraints excluded: chain v residue 43 ASN Chi-restraints excluded: chain v residue 89 MET Chi-restraints excluded: chain w residue 3 LEU Chi-restraints excluded: chain w residue 24 SER Chi-restraints excluded: chain w residue 68 ASP Chi-restraints excluded: chain y residue 4 LYS Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 22 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 61 ARG Chi-restraints excluded: chain 1 residue 15 LEU Chi-restraints excluded: chain 1 residue 70 LYS Chi-restraints excluded: chain 2 residue 5 LYS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 16 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 589 optimal weight: 6.9990 chunk 790 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 683 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 chunk 742 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 762 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS F 5 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 93 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN U 46 GLN b 45 GLN m 78 ASN m 146 ASN ** n 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 HIS ** s 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 ASN ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 35 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.183121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.144701 restraints weight = 114851.243| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.30 r_work: 0.3303 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.3161 rms_B_bonded: 3.86 restraints_weight: 0.1250 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 152207 Z= 0.364 Angle : 0.996 10.762 229001 Z= 0.486 Chirality : 0.050 0.336 29444 Planarity : 0.008 0.102 11367 Dihedral : 23.898 179.968 79419 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 3.75 % Allowed : 17.84 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 4751 helix: -0.22 (0.12), residues: 1532 sheet: -0.92 (0.16), residues: 939 loop : -1.06 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 248 HIS 0.016 0.003 HIS E 165 PHE 0.028 0.004 PHE 1 10 TYR 0.032 0.004 TYR j 213 ARG 0.014 0.002 ARG o 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44064.88 seconds wall clock time: 763 minutes 43.34 seconds (45823.34 seconds total)