Starting phenix.real_space_refine on Sat Mar 23 23:24:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/03_2024/3jcn_3285_neut_trim_updated.pdb" } resolution = 4.6 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= 0.072 sd= 0.559 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4640 5.49 5 S 161 5.16 5 C 74306 2.51 5 N 27411 2.21 5 O 40774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" 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 ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" 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 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "W PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "b ARG 390": "NH1" <-> "NH2" Residue "b ARG 412": "NH1" <-> "NH2" Residue "b ARG 455": "NH1" <-> "NH2" Residue "b ARG 561": "NH1" <-> "NH2" Residue "b ARG 587": "NH1" <-> "NH2" Residue "b ARG 605": "NH1" <-> "NH2" Residue "b ARG 607": "NH1" <-> "NH2" Residue "b ARG 610": "NH1" <-> "NH2" Residue "b ARG 662": "NH1" <-> "NH2" Residue "b ARG 668": "NH1" <-> "NH2" Residue "b ARG 766": "NH1" <-> "NH2" Residue "b ARG 829": "NH1" <-> "NH2" Residue "b ARG 846": "NH1" <-> "NH2" Residue "b GLU 884": "OE1" <-> "OE2" Residue "b ARG 887": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 123": "NH1" <-> "NH2" Residue "o ARG 55": "NH1" <-> "NH2" Residue "s ARG 28": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147292 Number of models: 1 Model: "" Number of chains: 57 Chain: "0" 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: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "3" 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: "4" 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: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 276, 'rna2p_pyr': 148, 'rna3p_pur': 1396, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 424, 'rna3p': 2472} Chain breaks: 1 Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2546 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, '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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 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: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 86, 'rna3p_pur': 754, 'rna3p_pyr': 579} Link IDs: {'rna2p': 206, 'rna3p': 1332} Chain: "b" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3847 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 491} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "f" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "g" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "h" 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: "i" 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: "j" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" 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: "l" 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: "m" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "n" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "o" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "p" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "q" 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: "r" 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: "s" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "t" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "u" 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: "v" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p': 1, 'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "x" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 56.23, per 1000 atoms: 0.38 Number of scatterers: 147292 At special positions: 0 Unit cell: (265.68, 282.9, 223.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 161 16.00 P 4640 15.00 O 40774 8.00 N 27411 7.00 C 74306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 815 " - pdb=" SG CYS b 861 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.76 Conformation dependent library (CDL) restraints added in 7.1 seconds 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11228 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: 183 helices and 68 sheets defined 37.3% alpha, 17.0% beta 1260 base pairs and 2600 stacking pairs defined. Time for finding SS restraints: 75.34 Creating SS restraints... Processing helix chain '0' and resid 8 through 20 removed outlier: 4.908A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix No H-bonds generated for 'chain '1' and resid 25 through 30' Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.243A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 4.145A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 removed outlier: 3.708A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.575A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.127A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 16' Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.880A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.501A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.646A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.917A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.798A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.036A pdb=" N HIS C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 201' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.478A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.584A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.639A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.534A pdb=" N ARG D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.982A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.559A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.542A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.799A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.684A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'F' and resid 1 through 20 removed outlier: 3.522A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.582A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 60 removed outlier: 3.703A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 109 removed outlier: 3.829A pdb=" N GLU F 100 " --> pdb=" O TRP F 96 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.867A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.039A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.650A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.710A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 152 " --> pdb=" O ARG G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.153A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 45 removed outlier: 3.672A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.248A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 74 through 82' Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.044A pdb=" N ASP I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS I 96 " --> pdb=" O PRO I 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 91 through 96' Processing helix chain 'I' and resid 101 through 112 removed outlier: 5.156A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 101 through 112' Processing helix chain 'I' and resid 120 through 134 removed outlier: 4.071A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 129 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 removed outlier: 5.976A pdb=" N LYS J 12 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.226A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.624A 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 123 removed outlier: 3.847A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 4.056A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.297A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.567A pdb=" N LEU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER K 109 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.504A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 69 through 74 removed outlier: 3.715A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.129A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.447A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.729A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.512A pdb=" N ARG M 50 " --> pdb=" O ILE M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.902A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.600A 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 removed outlier: 3.545A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 3.742A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.783A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.648A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG N 71 " --> pdb=" O PHE N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 3.729A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU N 82 " --> pdb=" O LYS N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.074A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.699A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.583A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.943A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.545A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 103 removed outlier: 4.131A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.523A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.506A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 56 removed outlier: 4.291A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 72 removed outlier: 3.597A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.501A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.585A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 3.524A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.690A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.578A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.527A pdb=" N LYS S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.551A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.919A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.612A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.587A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.900A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.557A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.596A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.767A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.607A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 9 removed outlier: 3.868A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.596A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 63 removed outlier: 4.467A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS Y 60 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.679A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 403 through 413 removed outlier: 3.901A pdb=" N LEU b 408 " --> pdb=" O LYS b 404 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 463 removed outlier: 3.873A pdb=" N ARG b 455 " --> pdb=" O PHE b 451 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA b 456 " --> pdb=" O THR b 452 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN b 460 " --> pdb=" O ALA b 456 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR b 462 " --> pdb=" O GLY b 458 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 490 removed outlier: 3.503A pdb=" N GLN b 484 " --> pdb=" O ILE b 480 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS b 485 " --> pdb=" O GLU b 481 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA b 489 " --> pdb=" O HIS b 485 " (cutoff:3.500A) Processing helix chain 'b' and resid 506 through 518 removed outlier: 4.088A pdb=" N VAL b 510 " --> pdb=" O ASP b 506 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN b 516 " --> pdb=" O ASN b 512 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR b 517 " --> pdb=" O GLU b 513 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY b 518 " --> pdb=" O LEU b 514 " (cutoff:3.500A) Processing helix chain 'b' and resid 540 through 556 removed outlier: 5.818A pdb=" N LEU b 544 " --> pdb=" O GLY b 540 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU b 555 " --> pdb=" O GLN b 551 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU b 556 " --> pdb=" O ALA b 552 " (cutoff:3.500A) Processing helix chain 'b' and resid 648 through 676 removed outlier: 4.342A pdb=" N GLU b 652 " --> pdb=" O LYS b 648 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL b 653 " --> pdb=" O LYS b 649 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS b 673 " --> pdb=" O GLN b 669 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN b 676 " --> pdb=" O SER b 672 " (cutoff:3.500A) Processing helix chain 'b' and resid 697 through 713 removed outlier: 4.063A pdb=" N VAL b 701 " --> pdb=" O VAL b 697 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU b 702 " --> pdb=" O GLN b 698 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA b 703 " --> pdb=" O GLY b 699 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER b 705 " --> pdb=" O VAL b 701 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP b 706 " --> pdb=" O GLU b 702 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER b 707 " --> pdb=" O ALA b 703 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU b 711 " --> pdb=" O SER b 707 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER b 712 " --> pdb=" O LEU b 708 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR b 713 " --> pdb=" O LEU b 709 " (cutoff:3.500A) Processing helix chain 'b' and resid 729 through 740 removed outlier: 3.911A pdb=" N SER b 739 " --> pdb=" O LEU b 735 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN b 740 " --> pdb=" O ALA b 736 " (cutoff:3.500A) Processing helix chain 'b' and resid 751 through 762 removed outlier: 3.927A pdb=" N LYS b 756 " --> pdb=" O ALA b 752 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL b 757 " --> pdb=" O SER b 753 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER b 762 " --> pdb=" O ILE b 758 " (cutoff:3.500A) Processing helix chain 'b' and resid 770 through 786 removed outlier: 3.734A pdb=" N LEU b 774 " --> pdb=" O VAL b 770 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU b 777 " --> pdb=" O ASN b 773 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS b 779 " --> pdb=" O ILE b 775 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU b 786 " --> pdb=" O MET b 782 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 14 removed outlier: 4.643A pdb=" N GLY c 12 " --> pdb=" O GLY c 8 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE c 13 " --> pdb=" O ILE c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.505A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE c 36 " --> pdb=" O LEU c 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.843A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.659A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.691A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.967A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN c 139 " --> pdb=" O ARG c 135 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY c 144 " --> pdb=" O ALA c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 28 Proline residue: d 28 - end of helix Processing helix chain 'd' and resid 42 through 63 removed outlier: 3.574A pdb=" N VAL d 46 " --> pdb=" O LEU d 42 " (cutoff:3.500A) Proline residue: d 47 - end of helix removed outlier: 3.929A pdb=" N ASN d 57 " --> pdb=" O LEU d 53 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE d 59 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA d 60 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER d 61 " --> pdb=" O ASN d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 Processing helix chain 'd' and resid 104 through 122 removed outlier: 4.717A pdb=" N GLN d 108 " --> pdb=" O LYS d 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER d 109 " --> pdb=" O THR d 105 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN d 119 " --> pdb=" O ASP d 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP d 122 " --> pdb=" O THR d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 147 removed outlier: 4.422A pdb=" N ARG d 136 " --> pdb=" O GLU d 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU d 139 " --> pdb=" O MET d 135 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU d 140 " --> pdb=" O ARG d 136 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN d 145 " --> pdb=" O GLU d 141 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER d 146 " --> pdb=" O LYS d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 154 removed outlier: 5.747A pdb=" N ASP d 152 " --> pdb=" O GLY d 148 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET d 153 " --> pdb=" O GLY d 149 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY d 154 " --> pdb=" O ILE d 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 148 through 154' Processing helix chain 'd' and resid 168 through 179 removed outlier: 3.840A pdb=" N GLU d 174 " --> pdb=" O ILE d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 222 removed outlier: 3.687A pdb=" N VAL d 209 " --> pdb=" O ALA d 205 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR d 212 " --> pdb=" O ALA d 208 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR d 219 " --> pdb=" O ALA d 215 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL d 220 " --> pdb=" O VAL d 216 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG d 221 " --> pdb=" O ALA d 217 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU d 222 " --> pdb=" O ALA d 218 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 81 removed outlier: 4.234A pdb=" N LYS d 80 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP d 81 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 70 removed outlier: 3.634A pdb=" N GLN f 60 " --> pdb=" O PRO f 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG f 67 " --> pdb=" O MET f 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG f 68 " --> pdb=" O GLU f 64 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASN f 69 " --> pdb=" O LYS f 65 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N MET f 70 " --> pdb=" O ALA f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 108 through 118 removed outlier: 7.105A pdb=" N ALA f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU f 114 " --> pdb=" O MET f 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 153 removed outlier: 3.624A pdb=" N VAL f 136 " --> pdb=" O PRO f 132 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG f 137 " --> pdb=" O ILE f 133 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA f 138 " --> pdb=" O ASN f 134 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR f 139 " --> pdb=" O VAL f 135 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE f 140 " --> pdb=" O VAL f 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN f 147 " --> pdb=" O LEU f 143 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER f 148 " --> pdb=" O GLU f 144 " (cutoff:3.500A) Proline residue: f 149 - end of helix removed outlier: 3.979A pdb=" N ALA f 153 " --> pdb=" O PRO f 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 6 through 15 removed outlier: 3.848A pdb=" N LEU g 10 " --> pdb=" O PRO g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 65 removed outlier: 3.509A pdb=" N VAL g 52 " --> pdb=" O SER g 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN g 53 " --> pdb=" O ASP g 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS g 57 " --> pdb=" O GLN g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 82 removed outlier: 3.676A pdb=" N ASN g 73 " --> pdb=" O ARG g 69 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR g 74 " --> pdb=" O GLN g 70 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS g 82 " --> pdb=" O ALA g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 96 removed outlier: 3.659A pdb=" N LEU g 90 " --> pdb=" O GLY g 86 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG g 96 " --> pdb=" O LEU g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 105 removed outlier: 3.583A pdb=" N GLY g 105 " --> pdb=" O VAL g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 109 through 120 removed outlier: 3.558A pdb=" N HIS g 119 " --> pdb=" O GLN g 115 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS g 120 " --> pdb=" O LEU g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 151 through 165 removed outlier: 3.525A pdb=" N ALA g 157 " --> pdb=" O ARG g 153 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU g 162 " --> pdb=" O LEU g 158 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN g 163 " --> pdb=" O GLU g 159 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG g 164 " --> pdb=" O LEU g 160 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU g 165 " --> pdb=" O ALA g 161 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 191 removed outlier: 3.610A pdb=" N LEU g 190 " --> pdb=" O GLU g 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER g 191 " --> pdb=" O ARG g 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 186 through 191' Processing helix chain 'g' and resid 195 through 205 removed outlier: 4.060A pdb=" N ILE g 199 " --> pdb=" O ASN g 195 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU g 202 " --> pdb=" O LEU g 198 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR g 203 " --> pdb=" O ILE g 199 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER g 204 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS g 205 " --> pdb=" O GLU g 201 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 30 removed outlier: 3.566A pdb=" N ALA h 23 " --> pdb=" O SER h 19 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS h 24 " --> pdb=" O GLU h 20 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN h 27 " --> pdb=" O ALA h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 54 removed outlier: 3.527A pdb=" N ILE h 41 " --> pdb=" O THR h 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 69 removed outlier: 4.182A pdb=" N PHE h 61 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL h 68 " --> pdb=" O ALA h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 91 through 111 removed outlier: 3.807A pdb=" N ASN h 96 " --> pdb=" O PRO h 92 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA h 97 " --> pdb=" O VAL h 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG h 110 " --> pdb=" O ALA h 106 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY h 111 " --> pdb=" O ALA h 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 127 removed outlier: 3.544A pdb=" N GLU h 122 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA h 127 " --> pdb=" O LEU h 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 131 through 148 removed outlier: 3.539A pdb=" N LYS h 135 " --> pdb=" O GLY h 131 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU h 138 " --> pdb=" O VAL h 134 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP h 139 " --> pdb=" O LYS h 135 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL h 140 " --> pdb=" O LYS h 136 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS h 141 " --> pdb=" O ARG h 137 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG h 142 " --> pdb=" O GLU h 138 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET h 143 " --> pdb=" O ASP h 139 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU h 145 " --> pdb=" O HIS h 141 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA h 146 " --> pdb=" O ARG h 142 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN h 147 " --> pdb=" O MET h 143 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS h 148 " --> pdb=" O ALA h 144 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 33 removed outlier: 3.949A pdb=" N VAL i 18 " --> pdb=" O GLN i 14 " (cutoff:3.500A) Proline residue: i 19 - end of helix removed outlier: 3.765A pdb=" N GLU i 23 " --> pdb=" O PRO i 19 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG i 24 " --> pdb=" O GLY i 20 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR i 26 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA i 28 " --> pdb=" O ARG i 24 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA i 32 " --> pdb=" O ALA i 28 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU i 33 " --> pdb=" O ILE i 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 82 removed outlier: 3.552A pdb=" N ASP i 72 " --> pdb=" O GLN i 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU i 73 " --> pdb=" O GLU i 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR i 76 " --> pdb=" O ASP i 72 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE i 78 " --> pdb=" O LEU i 74 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG i 79 " --> pdb=" O GLU i 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN i 81 " --> pdb=" O THR i 77 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP i 82 " --> pdb=" O PHE i 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 38 removed outlier: 4.095A pdb=" N PHE j 38 " --> pdb=" O LEU j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 45 through 53 Proline residue: j 50 - end of helix removed outlier: 5.020A pdb=" N LEU j 53 " --> pdb=" O GLN j 49 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 87 removed outlier: 3.575A pdb=" N GLN j 74 " --> pdb=" O GLY j 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR j 83 " --> pdb=" O ARG j 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG j 84 " --> pdb=" O HIS j 80 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N MET j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 removed outlier: 4.740A pdb=" N GLU j 96 " --> pdb=" O SER j 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS j 99 " --> pdb=" O SER j 95 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 20 removed outlier: 3.520A pdb=" N ASP k 8 " --> pdb=" O ASP k 4 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET k 9 " --> pdb=" O PRO k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 29 through 43 removed outlier: 3.770A pdb=" N ALA k 36 " --> pdb=" O LYS k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 119 Processing helix chain 'l' and resid 45 through 50 removed outlier: 3.859A pdb=" N GLY l 50 " --> pdb=" O ALA l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 58 removed outlier: 4.105A pdb=" N SER l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR l 58 " --> pdb=" O SER l 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 53 through 58' Processing helix chain 'l' and resid 59 through 74 removed outlier: 3.709A pdb=" N GLN l 63 " --> pdb=" O PRO l 59 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA l 72 " --> pdb=" O ARG l 68 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL l 73 " --> pdb=" O CYS l 69 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS l 74 " --> pdb=" O ALA l 70 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 103 removed outlier: 3.923A pdb=" N ILE l 96 " --> pdb=" O ARG l 92 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG l 97 " --> pdb=" O GLU l 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA l 98 " --> pdb=" O SER l 94 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU l 99 " --> pdb=" O THR l 95 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY l 103 " --> pdb=" O LEU l 99 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 33 removed outlier: 6.620A pdb=" N GLN m 20 " --> pdb=" O ARG m 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA m 21 " --> pdb=" O LEU m 17 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL m 26 " --> pdb=" O THR m 22 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU m 27 " --> pdb=" O ALA m 23 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG m 31 " --> pdb=" O GLU m 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 88 removed outlier: 3.582A pdb=" N ASP m 85 " --> pdb=" O GLU m 81 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA m 86 " --> pdb=" O LYS m 82 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU m 87 " --> pdb=" O THR m 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET m 88 " --> pdb=" O VAL m 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 21 removed outlier: 3.700A pdb=" N THR n 19 " --> pdb=" O VAL n 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE n 21 " --> pdb=" O ALA n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 37 removed outlier: 3.674A pdb=" N LEU n 33 " --> pdb=" O SER n 29 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 63 removed outlier: 3.590A pdb=" N ASP n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR n 54 " --> pdb=" O GLY n 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU n 55 " --> pdb=" O GLN n 51 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU n 58 " --> pdb=" O THR n 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE n 62 " --> pdb=" O GLU n 58 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 65 through 83 removed outlier: 3.806A pdb=" N LEU n 79 " --> pdb=" O SER n 75 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 93 removed outlier: 3.646A pdb=" N ARG n 91 " --> pdb=" O GLY n 87 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY n 93 " --> pdb=" O ARG n 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 105 through 110 removed outlier: 4.215A pdb=" N GLY n 110 " --> pdb=" O ALA n 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 105 through 110' Processing helix chain 'o' and resid 2 through 10 removed outlier: 3.549A pdb=" N LEU o 6 " --> pdb=" O THR o 2 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG o 8 " --> pdb=" O ASN o 4 " (cutoff:3.500A) Proline residue: o 10 - end of helix Processing helix chain 'o' and resid 112 through 117 removed outlier: 5.020A pdb=" N TYR o 116 " --> pdb=" O ALA o 112 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY o 117 " --> pdb=" O ARG o 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 112 through 117' Processing helix chain 'p' and resid 3 through 15 removed outlier: 3.540A pdb=" N ALA p 8 " --> pdb=" O THR p 4 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE p 10 " --> pdb=" O ALA p 6 " (cutoff:3.500A) Processing helix chain 'p' and resid 23 through 43 removed outlier: 3.593A pdb=" N LEU p 31 " --> pdb=" O GLN p 27 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY p 40 " --> pdb=" O ASN p 36 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS p 41 " --> pdb=" O HIS p 37 " (cutoff:3.500A) Processing helix chain 'p' and resid 48 through 73 removed outlier: 3.839A pdb=" N ARG p 52 " --> pdb=" O ASP p 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG p 53 " --> pdb=" O HIS p 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY p 54 " --> pdb=" O HIS p 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS p 64 " --> pdb=" O SER p 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG p 71 " --> pdb=" O ASP p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 85 Processing helix chain 'q' and resid 2 through 19 removed outlier: 3.904A pdb=" N ALA q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP q 17 " --> pdb=" O VAL q 13 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS q 18 " --> pdb=" O ALA q 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 30 removed outlier: 3.847A pdb=" N GLU q 25 " --> pdb=" O ALA q 21 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU q 26 " --> pdb=" O LYS q 22 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS q 27 " --> pdb=" O ARG q 23 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA q 28 " --> pdb=" O ALA q 24 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE q 29 " --> pdb=" O GLU q 25 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE q 30 " --> pdb=" O LEU q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 21 through 30' Processing helix chain 'q' and resid 43 through 49 removed outlier: 3.824A pdb=" N LYS q 47 " --> pdb=" O ASN q 43 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU q 48 " --> pdb=" O ALA q 44 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN q 49 " --> pdb=" O VAL q 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 43 through 49' Processing helix chain 'q' and resid 80 through 91 removed outlier: 3.553A pdb=" N ARG q 90 " --> pdb=" O GLU q 86 " (cutoff:3.500A) Processing helix chain 's' and resid 53 through 64 removed outlier: 3.502A pdb=" N ILE s 57 " --> pdb=" O ASP s 53 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS s 59 " --> pdb=" O ASP s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 68 through 79 Processing helix chain 't' and resid 11 through 24 Processing helix chain 't' and resid 69 through 75 removed outlier: 4.266A pdb=" N PHE t 73 " --> pdb=" O LYS t 69 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA t 74 " --> pdb=" O LEU t 70 " (cutoff:3.500A) Proline residue: t 75 - end of helix No H-bonds generated for 'chain 't' and resid 69 through 75' Processing helix chain 't' and resid 63 through 68 removed outlier: 3.723A pdb=" N VAL t 66 " --> pdb=" O ASP t 63 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY t 67 " --> pdb=" O GLU t 64 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 33 removed outlier: 5.073A pdb=" N ASN u 30 " --> pdb=" O ALA u 26 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR u 31 " --> pdb=" O THR u 27 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR u 33 " --> pdb=" O LYS u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 45 removed outlier: 3.636A pdb=" N THR u 44 " --> pdb=" O PRO u 40 " (cutoff:3.500A) Processing helix chain 'u' and resid 47 through 65 Processing helix chain 'w' and resid 17 through 22 Processing helix chain 'w' and resid 25 through 33 removed outlier: 4.365A pdb=" N ARG w 33 " --> pdb=" O ALA w 29 " (cutoff:3.500A) Processing helix chain 'w' and resid 36 through 52 Proline residue: w 40 - end of helix removed outlier: 3.572A pdb=" N ARG w 44 " --> pdb=" O PRO w 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS w 45 " --> pdb=" O THR w 41 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG w 46 " --> pdb=" O THR w 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA w 47 " --> pdb=" O GLU w 43 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS w 48 " --> pdb=" O ARG w 44 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL w 52 " --> pdb=" O LYS w 48 " (cutoff:3.500A) Processing helix chain 'x' and resid 7 through 39 removed outlier: 3.643A pdb=" N ILE x 11 " --> pdb=" O LYS x 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER x 22 " --> pdb=" O LYS x 18 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL x 34 " --> pdb=" O PHE x 30 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR x 35 " --> pdb=" O ILE x 31 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA x 36 " --> pdb=" O LYS x 32 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA x 37 " --> pdb=" O LYS x 33 " (cutoff:3.500A) Processing helix chain 'x' and resid 42 through 64 removed outlier: 3.634A pdb=" N ALA x 46 " --> pdb=" O ASP x 42 " (cutoff:3.500A) Proline residue: x 55 - end of helix removed outlier: 3.571A pdb=" N ASP x 58 " --> pdb=" O GLN x 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA x 61 " --> pdb=" O VAL x 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 67 through 86 removed outlier: 5.177A pdb=" N ALA x 71 " --> pdb=" O HIS x 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS x 75 " --> pdb=" O ALA x 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA x 80 " --> pdb=" O ALA x 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN x 83 " --> pdb=" O THR x 79 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS x 84 " --> pdb=" O ALA x 80 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU x 85 " --> pdb=" O GLN x 81 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA x 86 " --> pdb=" O ILE x 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 7 through 11 Processing sheet with id= 2, first strand: chain '1' and resid 32 through 38 removed outlier: 3.755A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR 1 48 " --> pdb=" O LEU 1 35 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS 1 37 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 21 through 24 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 5, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.761A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 115 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.537A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.142A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 163 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.253A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.744A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 79 through 84 removed outlier: 5.880A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 1 through 4 Processing sheet with id= 12, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.048A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 64 through 67 removed outlier: 3.791A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.597A pdb=" N ASP G 15 " --> pdb=" O LYS G 26 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN G 21 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 16, first strand: chain 'G' and resid 93 through 98 removed outlier: 3.539A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 116 " --> pdb=" O ASN G 100 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.819A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS G 85 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 7 through 10 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 20, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.602A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR J 78 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.749A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.570A pdb=" N TRP M 64 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.380A 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 36 removed outlier: 4.798A 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: 3.661A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS O 34 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.726A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 48 through 52 removed outlier: 4.297A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 2 through 6 removed outlier: 3.532A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 32 through 36 removed outlier: 7.364A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 39 through 42 removed outlier: 8.674A pdb=" N LEU R 39 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.261A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.974A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'T' and resid 28 through 33 removed outlier: 8.515A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 8 through 11 removed outlier: 4.386A pdb=" N ASP U 8 " --> pdb=" O VAL U 24 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 40 through 44 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.978A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 41 through 44 removed outlier: 6.378A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.730A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 11 through 17 removed outlier: 3.701A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Z' and resid 34 through 38 removed outlier: 7.881A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'b' and resid 428 through 432 removed outlier: 4.034A pdb=" N GLY b 429 " --> pdb=" O ASP b 444 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP b 444 " --> pdb=" O GLY b 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR b 441 " --> pdb=" O PRO b 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL b 394 " --> pdb=" O THR b 441 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR b 445 " --> pdb=" O ILE b 396 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY b 398 " --> pdb=" O THR b 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA b 496 " --> pdb=" O LEU b 467 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'b' and resid 571 through 575 removed outlier: 3.555A pdb=" N GLU b 571 " --> pdb=" O THR b 583 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR b 583 " --> pdb=" O ILE b 570 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER b 566 " --> pdb=" O ARG b 587 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA b 565 " --> pdb=" O VAL b 643 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP b 639 " --> pdb=" O VAL b 569 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE b 596 " --> pdb=" O VAL b 644 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'b' and resid 608 through 611 removed outlier: 4.030A pdb=" N ALA b 608 " --> pdb=" O LEU b 629 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU b 629 " --> pdb=" O ALA b 608 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 717 through 721 removed outlier: 3.645A pdb=" N LYS b 719 " --> pdb=" O VAL b 689 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU b 693 " --> pdb=" O ILE b 721 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE b 742 " --> pdb=" O ASN b 690 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE b 746 " --> pdb=" O LYS b 694 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP b 764 " --> pdb=" O ALA b 741 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY b 745 " --> pdb=" O ARG b 766 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 798 through 801 Processing sheet with id= 46, first strand: chain 'b' and resid 820 through 824 removed outlier: 6.924A pdb=" N GLY b 820 " --> pdb=" O ASN b 857 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ASN b 853 " --> pdb=" O ARG b 824 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 827 through 830 Processing sheet with id= 48, first strand: chain 'b' and resid 812 through 816 Processing sheet with id= 49, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.755A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU c 57 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN c 101 " --> pdb=" O VAL c 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 166 through 170 removed outlier: 3.664A pdb=" N SER c 153 " --> pdb=" O GLY c 196 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE c 195 " --> pdb=" O ALA c 188 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 29 through 32 removed outlier: 7.337A pdb=" N PHE d 29 " --> pdb=" O ASN d 41 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE d 39 " --> pdb=" O PHE d 31 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 88 through 92 removed outlier: 6.417A pdb=" N PHE d 89 " --> pdb=" O ILE d 66 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU d 67 " --> pdb=" O ALA d 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL d 162 " --> pdb=" O PHE d 183 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 10 through 15 removed outlier: 4.083A pdb=" N GLN f 11 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU f 35 " --> pdb=" O ILE f 15 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 82 through 87 removed outlier: 8.037A pdb=" N HIS f 82 " --> pdb=" O PRO f 97 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL f 84 " --> pdb=" O MET f 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET f 95 " --> pdb=" O VAL f 84 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 31 through 39 removed outlier: 4.642A pdb=" N ALA f 34 " --> pdb=" O GLY f 50 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY f 50 " --> pdb=" O ALA f 34 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 140 through 143 removed outlier: 4.060A pdb=" N ASP g 140 " --> pdb=" O PHE g 181 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 72 through 78 removed outlier: 6.396A pdb=" N TYR h 84 " --> pdb=" O ARG h 77 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 39 through 43 removed outlier: 3.552A pdb=" N VAL i 10 " --> pdb=" O HIS i 58 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL i 60 " --> pdb=" O PHE i 8 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE i 6 " --> pdb=" O MET i 62 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS i 3 " --> pdb=" O THR i 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR i 92 " --> pdb=" O HIS i 3 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG i 86 " --> pdb=" O MET i 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 5 through 10 removed outlier: 4.569A pdb=" N GLY j 9 " --> pdb=" O ALA j 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR j 65 " --> pdb=" O ARG j 17 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 22 through 27 removed outlier: 6.004A pdb=" N ALA k 22 " --> pdb=" O LEU k 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.616A pdb=" N VAL k 102 " --> pdb=" O ILE k 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS k 126 " --> pdb=" O VAL k 102 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 41 through 44 removed outlier: 3.689A pdb=" N GLU l 82 " --> pdb=" O GLY l 18 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN l 108 " --> pdb=" O LEU l 81 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY l 87 " --> pdb=" O VAL l 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 36 through 42 removed outlier: 6.602A pdb=" N VAL m 36 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL m 77 " --> pdb=" O VAL m 36 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY m 38 " --> pdb=" O ASP m 75 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP m 75 " --> pdb=" O GLY m 38 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU m 42 " --> pdb=" O LEU m 71 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU m 71 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG m 72 " --> pdb=" O LEU m 10 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL m 74 " --> pdb=" O ILE m 8 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE m 8 " --> pdb=" O VAL m 74 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE m 76 " --> pdb=" O ILE m 6 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE m 6 " --> pdb=" O ILE m 76 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG m 7 " --> pdb=" O SER m 101 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'o' and resid 28 through 32 removed outlier: 4.978A pdb=" N LEU o 80 " --> pdb=" O VAL o 97 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS o 95 " --> pdb=" O ARG o 82 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 35 through 40 removed outlier: 4.217A pdb=" N ARG o 35 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS o 50 " --> pdb=" O ILE o 66 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE o 60 " --> pdb=" O LEU o 56 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 19 through 27 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 's' and resid 4 through 8 Processing sheet with id= 68, first strand: chain 't' and resid 47 through 51 removed outlier: 3.539A pdb=" N ILE t 48 " --> pdb=" O VAL t 59 " (cutoff:3.500A) 1541 hydrogen bonds defined for protein. 4545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3047 hydrogen bonds 4848 hydrogen bond angles 0 basepair planarities 1260 basepair parallelities 2600 stacking parallelities Total time for adding SS restraints: 236.97 Time building geometry restraints manager: 66.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18540 1.33 - 1.45: 68857 1.45 - 1.57: 62912 1.57 - 1.69: 9274 1.69 - 1.81: 291 Bond restraints: 159874 Sorted by residual: bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1' GNP b 901 " pdb=" C2' GNP b 901 " ideal model delta sigma weight residual 1.273 1.521 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3' GNP b 901 " pdb=" C4' GNP b 901 " ideal model delta sigma weight residual 1.285 1.520 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C5 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.155 1.387 -0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 159869 not shown) Histogram of bond angle deviations from ideal: 73.13 - 86.72: 1 86.72 - 100.31: 47 100.31 - 113.90: 121433 113.90 - 127.49: 108285 127.49 - 141.08: 9077 Bond angle restraints: 238843 Sorted by residual: angle pdb=" O3' A z 14 " pdb=" C3' A z 14 " pdb=" C2' A z 14 " ideal model delta sigma weight residual 113.70 133.78 -20.08 1.50e+00 4.44e-01 1.79e+02 angle pdb=" OP2 U z 15 " pdb=" P U z 15 " pdb=" O5' U z 15 " ideal model delta sigma weight residual 108.00 73.13 34.87 3.00e+00 1.11e-01 1.35e+02 angle pdb=" OP1 U z 15 " pdb=" P U z 15 " pdb=" O5' U z 15 " ideal model delta sigma weight residual 108.00 141.08 -33.08 3.00e+00 1.11e-01 1.22e+02 angle pdb=" O3' C v 23 " pdb=" C3' C v 23 " pdb=" C2' C v 23 " ideal model delta sigma weight residual 113.70 97.78 15.92 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C4' A z 13 " pdb=" C3' A z 13 " pdb=" O3' A z 13 " ideal model delta sigma weight residual 113.00 97.10 15.90 1.50e+00 4.44e-01 1.12e+02 ... (remaining 238838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 92255 35.69 - 71.37: 8857 71.37 - 107.06: 1216 107.06 - 142.75: 8 142.75 - 178.43: 20 Dihedral angle restraints: 102356 sinusoidal: 84937 harmonic: 17419 Sorted by residual: dihedral pdb=" C5' U A1344 " pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" O3' U A1344 " ideal model delta sinusoidal sigma weight residual 147.00 74.55 72.45 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' U A1344 " pdb=" C3' U A1344 " pdb=" C2' U A1344 " pdb=" C1' U A1344 " ideal model delta sinusoidal sigma weight residual -35.00 34.14 -69.14 1 8.00e+00 1.56e-02 9.66e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 54.34 145.66 1 1.50e+01 4.44e-03 7.79e+01 ... (remaining 102353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 30300 0.253 - 0.505: 175 0.505 - 0.758: 6 0.758 - 1.011: 1 1.011 - 1.263: 1 Chirality restraints: 30483 Sorted by residual: chirality pdb=" C3' A z 14 " pdb=" C4' A z 14 " pdb=" O3' A z 14 " pdb=" C2' A z 14 " both_signs ideal model delta sigma weight residual False -2.48 -1.21 -1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C4' A z 16 " pdb=" C5' A z 16 " pdb=" O4' A z 16 " pdb=" C3' A z 16 " both_signs ideal model delta sigma weight residual False -2.50 -1.71 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" C3' 4SU v 8 " pdb=" C4' 4SU v 8 " pdb=" O3' 4SU v 8 " pdb=" C2' 4SU v 8 " both_signs ideal model delta sigma weight residual False -2.48 -1.77 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 30480 not shown) Planarity restraints: 13036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U v 20 " -0.395 2.00e-02 2.50e+03 3.94e-01 3.49e+03 pdb=" C4' H2U v 20 " 0.351 2.00e-02 2.50e+03 pdb=" O4' H2U v 20 " 0.579 2.00e-02 2.50e+03 pdb=" C3' H2U v 20 " -0.438 2.00e-02 2.50e+03 pdb=" O3' H2U v 20 " 0.188 2.00e-02 2.50e+03 pdb=" C2' H2U v 20 " -0.430 2.00e-02 2.50e+03 pdb=" O2' H2U v 20 " 0.180 2.00e-02 2.50e+03 pdb=" C1' H2U v 20 " 0.391 2.00e-02 2.50e+03 pdb=" N1 H2U v 20 " -0.427 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU v 54 " -0.393 2.00e-02 2.50e+03 3.89e-01 3.41e+03 pdb=" C4' 5MU v 54 " 0.355 2.00e-02 2.50e+03 pdb=" O4' 5MU v 54 " 0.583 2.00e-02 2.50e+03 pdb=" C3' 5MU v 54 " -0.437 2.00e-02 2.50e+03 pdb=" O3' 5MU v 54 " 0.193 2.00e-02 2.50e+03 pdb=" C2' 5MU v 54 " -0.442 2.00e-02 2.50e+03 pdb=" O2' 5MU v 54 " 0.179 2.00e-02 2.50e+03 pdb=" C1' 5MU v 54 " 0.360 2.00e-02 2.50e+03 pdb=" N1 5MU v 54 " -0.398 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP b 901 " -0.359 2.00e-02 2.50e+03 3.87e-01 3.38e+03 pdb=" C2' GNP b 901 " 0.439 2.00e-02 2.50e+03 pdb=" C3' GNP b 901 " 0.442 2.00e-02 2.50e+03 pdb=" C4' GNP b 901 " -0.358 2.00e-02 2.50e+03 pdb=" C5' GNP b 901 " 0.385 2.00e-02 2.50e+03 pdb=" N9 GNP b 901 " 0.398 2.00e-02 2.50e+03 pdb=" O2' GNP b 901 " -0.192 2.00e-02 2.50e+03 pdb=" O3' GNP b 901 " -0.183 2.00e-02 2.50e+03 pdb=" O4' GNP b 901 " -0.572 2.00e-02 2.50e+03 ... (remaining 13033 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 11 2.06 - 2.77: 17675 2.77 - 3.48: 195071 3.48 - 4.19: 472126 4.19 - 4.90: 630547 Nonbonded interactions: 1315430 Sorted by model distance: nonbonded pdb=" O SER b 534 " pdb=" O6 GNP b 901 " model vdw 1.344 3.040 nonbonded pdb=" O4' A a1339 " pdb=" O2' C v 41 " model vdw 1.381 2.440 nonbonded pdb=" O LYS G 175 " pdb=" O LYS G 176 " model vdw 1.423 3.040 nonbonded pdb=" O2* PSU v 55 " pdb=" O5' C v 56 " model vdw 1.485 3.040 nonbonded pdb=" OP2 U a1506 " pdb=" OP1 A z 13 " model vdw 1.796 3.040 ... (remaining 1315425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.160 Extract box with map and model: 12.120 Check model and map are aligned: 1.650 Set scattering table: 1.060 Process input model: 537.310 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 559.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.318 159874 Z= 0.466 Angle : 1.082 34.870 238843 Z= 0.718 Chirality : 0.098 1.263 30483 Planarity : 0.008 0.394 13036 Dihedral : 21.431 178.433 91125 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 1.48 % Allowed : 6.93 % Favored : 91.59 % Rotamer: Outliers : 0.18 % Allowed : 2.60 % Favored : 97.22 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.09), residues: 6020 helix: -2.52 (0.09), residues: 1640 sheet: -2.11 (0.14), residues: 888 loop : -2.24 (0.09), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 21 HIS 0.010 0.002 HIS J 80 PHE 0.025 0.002 PHE I 68 TYR 0.018 0.002 TYR j 6 ARG 0.012 0.001 ARG 2 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2185 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2176 time to evaluate : 6.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 GLN cc_start: 0.7469 (mt0) cc_final: 0.7220 (mt0) REVERT: 0 43 THR cc_start: 0.7874 (p) cc_final: 0.7168 (p) REVERT: 2 16 HIS cc_start: 0.6345 (m-70) cc_final: 0.5984 (m-70) REVERT: 2 22 MET cc_start: 0.6957 (tpp) cc_final: 0.5814 (tpt) REVERT: 3 12 ARG cc_start: 0.7516 (mtt90) cc_final: 0.7154 (mtm-85) REVERT: C 43 ASN cc_start: 0.7249 (p0) cc_final: 0.6299 (p0) REVERT: C 59 GLN cc_start: 0.7645 (mt0) cc_final: 0.7186 (mt0) REVERT: C 103 ILE cc_start: 0.8387 (pt) cc_final: 0.7769 (pt) REVERT: C 117 SER cc_start: 0.8428 (p) cc_final: 0.8087 (t) REVERT: C 201 LEU cc_start: 0.8247 (mp) cc_final: 0.7943 (mp) REVERT: C 204 LEU cc_start: 0.6424 (mp) cc_final: 0.6216 (mt) REVERT: C 218 THR cc_start: 0.6601 (m) cc_final: 0.5922 (p) REVERT: C 239 PHE cc_start: 0.7689 (t80) cc_final: 0.7372 (t80) REVERT: C 256 THR cc_start: 0.7053 (p) cc_final: 0.6727 (p) REVERT: C 265 PHE cc_start: 0.4628 (m-80) cc_final: 0.4425 (m-10) REVERT: D 26 VAL cc_start: 0.7867 (t) cc_final: 0.7205 (t) REVERT: D 43 ASP cc_start: 0.5147 (m-30) cc_final: 0.4757 (m-30) REVERT: D 67 HIS cc_start: 0.5989 (t-90) cc_final: 0.5167 (t70) REVERT: D 91 THR cc_start: 0.6797 (p) cc_final: 0.6207 (m) REVERT: E 1 MET cc_start: 0.4387 (ptm) cc_final: 0.2907 (ttp) REVERT: E 92 HIS cc_start: 0.5147 (m-70) cc_final: 0.4651 (m-70) REVERT: E 98 LYS cc_start: 0.7995 (mttm) cc_final: 0.7668 (mmmt) REVERT: E 99 LYS cc_start: 0.8453 (mttt) cc_final: 0.7902 (mtpt) REVERT: E 193 VAL cc_start: 0.8057 (t) cc_final: 0.7486 (p) REVERT: F 13 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7194 (tttm) REVERT: F 47 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6566 (tttp) REVERT: F 51 ASN cc_start: 0.4916 (m-40) cc_final: 0.4643 (t0) REVERT: F 95 MET cc_start: 0.7574 (ttp) cc_final: 0.6307 (ttt) REVERT: F 127 TYR cc_start: 0.3437 (t80) cc_final: 0.2954 (t80) REVERT: G 32 LEU cc_start: 0.6222 (mp) cc_final: 0.5500 (mp) REVERT: H 1 MET cc_start: 0.4593 (ptm) cc_final: 0.3557 (ptp) REVERT: J 36 LEU cc_start: 0.8674 (mt) cc_final: 0.7216 (mt) REVERT: J 44 TYR cc_start: 0.7947 (t80) cc_final: 0.7051 (t80) REVERT: J 68 LYS cc_start: 0.8086 (mttt) cc_final: 0.7823 (mttp) REVERT: J 113 PRO cc_start: 0.8717 (Cg_exo) cc_final: 0.8485 (Cg_endo) REVERT: J 124 VAL cc_start: 0.8142 (m) cc_final: 0.7535 (m) REVERT: J 125 TYR cc_start: 0.6996 (m-80) cc_final: 0.6725 (m-10) REVERT: K 6 THR cc_start: 0.8045 (m) cc_final: 0.7579 (p) REVERT: K 70 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7230 (ttm110) REVERT: L 58 TYR cc_start: 0.6607 (p90) cc_final: 0.5900 (p90) REVERT: M 82 MET cc_start: 0.8815 (mmp) cc_final: 0.8463 (mmt) REVERT: N 24 MET cc_start: 0.6573 (ttp) cc_final: 0.5696 (ttp) REVERT: N 34 ILE cc_start: 0.7011 (pt) cc_final: 0.6754 (pt) REVERT: O 39 VAL cc_start: 0.7597 (t) cc_final: 0.6819 (t) REVERT: O 67 ASN cc_start: 0.7102 (p0) cc_final: 0.6657 (p0) REVERT: P 24 THR cc_start: 0.5879 (m) cc_final: 0.5643 (p) REVERT: P 46 VAL cc_start: 0.8514 (t) cc_final: 0.8063 (p) REVERT: Q 51 GLN cc_start: 0.7061 (mt0) cc_final: 0.6085 (mt0) REVERT: Q 63 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7278 (mtt180) REVERT: Q 73 ILE cc_start: 0.6995 (tt) cc_final: 0.6792 (tt) REVERT: Q 97 ILE cc_start: 0.6084 (mt) cc_final: 0.5583 (mt) REVERT: R 5 PHE cc_start: 0.5941 (p90) cc_final: 0.5686 (p90) REVERT: R 14 VAL cc_start: 0.7742 (t) cc_final: 0.7348 (m) REVERT: S 36 LEU cc_start: 0.8342 (mt) cc_final: 0.8066 (mt) REVERT: S 71 VAL cc_start: 0.7775 (t) cc_final: 0.7572 (t) REVERT: S 94 ASP cc_start: 0.7521 (m-30) cc_final: 0.7312 (m-30) REVERT: T 19 LYS cc_start: 0.6727 (tttt) cc_final: 0.6499 (ttpt) REVERT: T 22 THR cc_start: 0.8522 (p) cc_final: 0.8254 (m) REVERT: T 39 THR cc_start: 0.7358 (m) cc_final: 0.6844 (p) REVERT: T 86 THR cc_start: 0.7438 (m) cc_final: 0.6730 (p) REVERT: U 42 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7483 (mmmt) REVERT: U 72 PHE cc_start: 0.5997 (t80) cc_final: 0.5236 (t80) REVERT: V 26 PHE cc_start: 0.7467 (p90) cc_final: 0.7263 (p90) REVERT: V 29 ILE cc_start: 0.8683 (tp) cc_final: 0.8281 (mm) REVERT: V 63 ILE cc_start: 0.8476 (mt) cc_final: 0.8064 (mt) REVERT: V 65 VAL cc_start: 0.5883 (p) cc_final: 0.5585 (p) REVERT: W 75 PHE cc_start: 0.7193 (m-80) cc_final: 0.6763 (m-80) REVERT: X 15 ASN cc_start: 0.7390 (m-40) cc_final: 0.6977 (m-40) REVERT: X 50 VAL cc_start: 0.8794 (m) cc_final: 0.8401 (p) REVERT: X 55 MET cc_start: 0.7136 (mtt) cc_final: 0.6924 (mtt) REVERT: Y 28 LEU cc_start: 0.8887 (mt) cc_final: 0.8073 (tp) REVERT: Y 42 LEU cc_start: 0.7909 (mt) cc_final: 0.7446 (mp) REVERT: Z 6 ILE cc_start: 0.7505 (mt) cc_final: 0.7300 (mt) REVERT: Z 40 THR cc_start: 0.6288 (p) cc_final: 0.6021 (t) REVERT: b 455 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6773 (ptm-80) REVERT: b 588 GLU cc_start: 0.6873 (mp0) cc_final: 0.5666 (tm-30) REVERT: b 642 THR cc_start: 0.5080 (p) cc_final: 0.3707 (p) REVERT: b 861 CYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5494 (p) REVERT: c 31 ASN cc_start: 0.7086 (t0) cc_final: 0.4970 (t0) REVERT: c 46 LEU cc_start: 0.7412 (mt) cc_final: 0.7154 (mt) REVERT: c 156 LEU cc_start: 0.6795 (mp) cc_final: 0.5733 (mp) REVERT: d 160 LEU cc_start: 0.7672 (tp) cc_final: 0.7198 (tp) REVERT: d 198 VAL cc_start: 0.6254 (p) cc_final: 0.5931 (m) REVERT: f 59 ILE cc_start: 0.8859 (pp) cc_final: 0.8617 (pt) REVERT: f 63 MET cc_start: 0.6735 (mmt) cc_final: 0.6175 (mmp) REVERT: f 93 VAL cc_start: 0.8347 (t) cc_final: 0.8064 (p) REVERT: f 116 VAL cc_start: 0.7362 (m) cc_final: 0.6945 (p) REVERT: f 151 MET cc_start: 0.7151 (mtm) cc_final: 0.6105 (tmm) REVERT: g 8 LEU cc_start: 0.7689 (mp) cc_final: 0.6948 (tp) REVERT: g 20 LEU cc_start: 0.7373 (mt) cc_final: 0.7108 (mt) REVERT: g 63 ILE cc_start: 0.7464 (mt) cc_final: 0.6755 (mm) REVERT: g 88 ASN cc_start: 0.7429 (m-40) cc_final: 0.6958 (m-40) REVERT: g 89 LEU cc_start: 0.7854 (tp) cc_final: 0.7458 (tp) REVERT: g 125 ASN cc_start: 0.7468 (m-40) cc_final: 0.6116 (t0) REVERT: g 141 VAL cc_start: 0.8039 (m) cc_final: 0.7267 (t) REVERT: h 90 VAL cc_start: 0.6308 (p) cc_final: 0.5780 (t) REVERT: i 1 MET cc_start: 0.0861 (tpp) cc_final: 0.0623 (tpp) REVERT: k 105 THR cc_start: 0.4537 (p) cc_final: 0.3827 (m) REVERT: o 3 VAL cc_start: 0.7564 (p) cc_final: 0.6604 (m) REVERT: o 72 ASN cc_start: 0.7421 (p0) cc_final: 0.6528 (t0) REVERT: p 84 LEU cc_start: 0.7096 (tp) cc_final: 0.6610 (tp) REVERT: q 70 PRO cc_start: 0.7693 (Cg_endo) cc_final: 0.7271 (Cg_exo) REVERT: r 40 THR cc_start: 0.6528 (m) cc_final: 0.6228 (p) REVERT: r 72 TRP cc_start: 0.6791 (m100) cc_final: 0.5541 (m100) REVERT: s 21 VAL cc_start: 0.7822 (t) cc_final: 0.7612 (m) REVERT: t 15 LEU cc_start: 0.8319 (tp) cc_final: 0.8038 (tp) REVERT: x 57 VAL cc_start: 0.8415 (t) cc_final: 0.7140 (t) outliers start: 9 outliers final: 2 residues processed: 2185 average time/residue: 1.5088 time to fit residues: 5405.0763 Evaluate side-chains 1538 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1535 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 6.9990 chunk 795 optimal weight: 6.9990 chunk 441 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 536 optimal weight: 1.9990 chunk 425 optimal weight: 5.9990 chunk 822 optimal weight: 30.0000 chunk 318 optimal weight: 10.0000 chunk 500 optimal weight: 5.9990 chunk 612 optimal weight: 3.9990 chunk 953 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 3 GLN 0 5 ASN 1 25 ASN 1 45 HIS 3 23 HIS 4 37 GLN C 52 HIS C 57 HIS C 142 ASN C 199 HIS C 225 ASN C 242 HIS C 250 GLN D 134 HIS D 150 GLN E 97 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN G 87 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 104 GLN N 73 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS O 104 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 40 ASN S 60 HIS S 61 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 35 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 19 HIS b 437 ASN b 448 HIS b 484 GLN ** b 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 886 GLN ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN d 38 HIS f 88 HIS f 96 GLN f 134 ASN g 135 GLN h 121 ASN ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 ASN ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 HIS ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN l 14 GLN m 99 GLN n 7 ASN n 51 GLN r 8 GLN ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS s 18 GLN ** x 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 159874 Z= 0.229 Angle : 0.675 19.566 238843 Z= 0.350 Chirality : 0.038 0.298 30483 Planarity : 0.006 0.115 13036 Dihedral : 22.476 179.034 79158 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.28 % Favored : 93.12 % Rotamer: Outliers : 0.26 % Allowed : 3.93 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.09), residues: 6020 helix: -0.92 (0.11), residues: 1779 sheet: -1.73 (0.14), residues: 1071 loop : -1.98 (0.10), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 212 HIS 0.015 0.002 HIS J 80 PHE 0.031 0.002 PHE r 27 TYR 0.033 0.002 TYR k 127 ARG 0.018 0.001 ARG Q 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1869 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1856 time to evaluate : 6.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 GLN cc_start: 0.7799 (mt0) cc_final: 0.7502 (mt0) REVERT: 0 30 ASP cc_start: 0.6765 (m-30) cc_final: 0.6418 (m-30) REVERT: 0 47 TYR cc_start: 0.5726 (m-10) cc_final: 0.5412 (m-10) REVERT: 2 16 HIS cc_start: 0.7230 (m-70) cc_final: 0.6779 (m-70) REVERT: C 43 ASN cc_start: 0.8171 (p0) cc_final: 0.7255 (p0) REVERT: C 57 HIS cc_start: 0.7146 (t-90) cc_final: 0.6815 (t70) REVERT: C 90 ILE cc_start: 0.8221 (pt) cc_final: 0.7963 (mp) REVERT: C 163 ILE cc_start: 0.7229 (tp) cc_final: 0.7002 (mp) REVERT: C 201 LEU cc_start: 0.8497 (mp) cc_final: 0.8250 (mp) REVERT: C 218 THR cc_start: 0.6250 (m) cc_final: 0.5974 (p) REVERT: C 229 HIS cc_start: 0.5848 (t-90) cc_final: 0.4457 (t-90) REVERT: D 67 HIS cc_start: 0.5965 (t-90) cc_final: 0.5752 (t-90) REVERT: D 91 THR cc_start: 0.7036 (p) cc_final: 0.6593 (m) REVERT: D 103 ASP cc_start: 0.7143 (p0) cc_final: 0.6684 (p0) REVERT: D 140 HIS cc_start: 0.7424 (m-70) cc_final: 0.7188 (m-70) REVERT: E 1 MET cc_start: 0.4528 (ptm) cc_final: 0.3111 (ttm) REVERT: E 72 SER cc_start: 0.7051 (t) cc_final: 0.6145 (m) REVERT: E 73 ILE cc_start: 0.7361 (tp) cc_final: 0.7127 (tp) REVERT: E 88 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7431 (mmm-85) REVERT: E 132 LYS cc_start: 0.8444 (pttt) cc_final: 0.8207 (pttt) REVERT: E 191 ASP cc_start: 0.4786 (t0) cc_final: 0.4476 (t0) REVERT: F 95 MET cc_start: 0.7875 (ttp) cc_final: 0.6800 (ttp) REVERT: G 76 ILE cc_start: 0.7499 (mp) cc_final: 0.7214 (tp) REVERT: G 104 LEU cc_start: 0.7940 (mt) cc_final: 0.7583 (mt) REVERT: G 143 VAL cc_start: 0.8860 (t) cc_final: 0.8616 (t) REVERT: H 1 MET cc_start: 0.4813 (ptm) cc_final: 0.4233 (ppp) REVERT: I 135 MET cc_start: 0.0372 (tmm) cc_final: -0.1749 (mpp) REVERT: J 52 ASP cc_start: 0.6784 (m-30) cc_final: 0.6203 (m-30) REVERT: J 77 HIS cc_start: 0.8095 (t-170) cc_final: 0.7843 (t-170) REVERT: J 89 PHE cc_start: 0.7562 (t80) cc_final: 0.7190 (t80) REVERT: J 113 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8521 (Cg_endo) REVERT: J 124 VAL cc_start: 0.7716 (m) cc_final: 0.7373 (m) REVERT: K 7 MET cc_start: 0.5064 (tpt) cc_final: 0.3305 (mtm) REVERT: K 41 ILE cc_start: 0.8301 (pt) cc_final: 0.8006 (pt) REVERT: K 76 VAL cc_start: 0.8661 (p) cc_final: 0.8443 (p) REVERT: K 118 LEU cc_start: 0.7760 (mt) cc_final: 0.6864 (mt) REVERT: L 136 GLU cc_start: 0.7752 (mp0) cc_final: 0.7525 (mp0) REVERT: M 82 MET cc_start: 0.8850 (mmp) cc_final: 0.8637 (mmt) REVERT: M 108 VAL cc_start: 0.8546 (m) cc_final: 0.8283 (m) REVERT: M 136 MET cc_start: 0.2815 (mtm) cc_final: 0.2598 (ptp) REVERT: N 24 MET cc_start: 0.7095 (ttp) cc_final: 0.6360 (ttp) REVERT: N 28 LEU cc_start: 0.8757 (tp) cc_final: 0.8478 (tt) REVERT: N 107 ASN cc_start: 0.7951 (t0) cc_final: 0.7555 (t0) REVERT: P 24 THR cc_start: 0.6115 (m) cc_final: 0.5842 (p) REVERT: P 110 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7405 (tptm) REVERT: Q 13 HIS cc_start: 0.7835 (m-70) cc_final: 0.7212 (m-70) REVERT: Q 14 LYS cc_start: 0.8410 (tppp) cc_final: 0.7826 (tppt) REVERT: Q 19 GLN cc_start: 0.7538 (mt0) cc_final: 0.7182 (mt0) REVERT: Q 23 TYR cc_start: 0.7669 (m-80) cc_final: 0.6976 (m-80) REVERT: Q 38 VAL cc_start: 0.8765 (t) cc_final: 0.8533 (p) REVERT: Q 47 ARG cc_start: 0.5932 (tmm-80) cc_final: 0.5172 (ttp-170) REVERT: Q 59 LEU cc_start: 0.8717 (tp) cc_final: 0.8409 (tp) REVERT: Q 101 ASP cc_start: 0.2949 (p0) cc_final: 0.2660 (p0) REVERT: Q 108 LEU cc_start: 0.8097 (mm) cc_final: 0.7867 (mm) REVERT: R 4 VAL cc_start: 0.8213 (t) cc_final: 0.7490 (t) REVERT: R 74 ILE cc_start: 0.8286 (mt) cc_final: 0.7892 (mt) REVERT: T 3 ARG cc_start: 0.5364 (ttm110) cc_final: 0.4140 (tpt-90) REVERT: T 19 LYS cc_start: 0.7484 (tttt) cc_final: 0.6925 (ttpt) REVERT: T 22 THR cc_start: 0.8821 (p) cc_final: 0.8603 (m) REVERT: T 40 LYS cc_start: 0.8653 (mttt) cc_final: 0.8319 (mttp) REVERT: V 12 GLN cc_start: 0.7609 (pm20) cc_final: 0.7100 (pm20) REVERT: V 26 PHE cc_start: 0.7638 (p90) cc_final: 0.7235 (p90) REVERT: V 41 GLU cc_start: 0.4712 (pm20) cc_final: 0.4369 (pm20) REVERT: V 42 LEU cc_start: 0.6180 (mm) cc_final: 0.5605 (mm) REVERT: V 65 VAL cc_start: 0.5873 (p) cc_final: 0.5623 (p) REVERT: W 15 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7299 (mtpt) REVERT: W 75 PHE cc_start: 0.7352 (m-80) cc_final: 0.6978 (m-80) REVERT: X 15 ASN cc_start: 0.7965 (m-40) cc_final: 0.7669 (m-40) REVERT: X 35 HIS cc_start: 0.4887 (t-170) cc_final: 0.4591 (t-90) REVERT: X 50 VAL cc_start: 0.9001 (m) cc_final: 0.8690 (p) REVERT: Y 37 LEU cc_start: 0.8652 (tt) cc_final: 0.7862 (tt) REVERT: Y 45 GLN cc_start: 0.6838 (pp30) cc_final: 0.6507 (pp30) REVERT: Z 6 ILE cc_start: 0.8039 (mt) cc_final: 0.7812 (mt) REVERT: Z 31 ILE cc_start: 0.9067 (mt) cc_final: 0.8782 (mt) REVERT: b 397 MET cc_start: 0.2913 (mpp) cc_final: 0.2606 (mpp) REVERT: b 399 HIS cc_start: 0.3588 (t-90) cc_final: 0.3331 (t-90) REVERT: b 550 LEU cc_start: 0.7385 (tt) cc_final: 0.6889 (pp) REVERT: b 661 PHE cc_start: 0.5392 (m-10) cc_final: 0.5170 (m-80) REVERT: b 677 MET cc_start: 0.4700 (pmm) cc_final: 0.4103 (ptm) REVERT: b 816 MET cc_start: 0.6896 (tpt) cc_final: 0.6532 (tpt) REVERT: b 867 ASN cc_start: 0.6911 (t0) cc_final: 0.6205 (t0) REVERT: c 131 ARG cc_start: 0.7461 (ptt90) cc_final: 0.6262 (ptt180) REVERT: c 156 LEU cc_start: 0.6970 (mp) cc_final: 0.6669 (mp) REVERT: c 202 PHE cc_start: 0.7097 (t80) cc_final: 0.6594 (t80) REVERT: d 62 ARG cc_start: 0.6357 (ttt-90) cc_final: 0.6029 (tmt170) REVERT: d 153 MET cc_start: 0.5285 (mtt) cc_final: 0.4961 (mtt) REVERT: f 63 MET cc_start: 0.7196 (mmt) cc_final: 0.6975 (mmt) REVERT: f 64 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6742 (tm-30) REVERT: f 65 LYS cc_start: 0.7622 (mttt) cc_final: 0.6899 (mttt) REVERT: f 82 HIS cc_start: 0.7285 (p90) cc_final: 0.6683 (p90) REVERT: f 116 VAL cc_start: 0.8224 (m) cc_final: 0.7732 (m) REVERT: f 151 MET cc_start: 0.7451 (mtm) cc_final: 0.6265 (tmm) REVERT: g 8 LEU cc_start: 0.7906 (mp) cc_final: 0.7449 (tp) REVERT: g 58 GLN cc_start: 0.7961 (mm-40) cc_final: 0.6748 (mm-40) REVERT: g 59 LYS cc_start: 0.7416 (tmtt) cc_final: 0.6905 (ttpp) REVERT: g 88 ASN cc_start: 0.7884 (m-40) cc_final: 0.7632 (m-40) REVERT: g 125 ASN cc_start: 0.7413 (m-40) cc_final: 0.6664 (t0) REVERT: g 141 VAL cc_start: 0.7754 (m) cc_final: 0.7157 (t) REVERT: g 165 GLU cc_start: 0.6302 (tm-30) cc_final: 0.5844 (tm-30) REVERT: g 190 LEU cc_start: 0.7552 (pp) cc_final: 0.7332 (pp) REVERT: h 100 MET cc_start: 0.6246 (mtp) cc_final: 0.5712 (ttp) REVERT: h 143 MET cc_start: 0.4178 (tmm) cc_final: 0.3707 (ppp) REVERT: j 80 HIS cc_start: 0.4722 (t-170) cc_final: 0.4456 (t70) REVERT: k 9 MET cc_start: 0.7558 (ttm) cc_final: 0.6739 (ttm) REVERT: k 91 LEU cc_start: 0.4677 (pt) cc_final: 0.4169 (pp) REVERT: k 105 THR cc_start: 0.5849 (p) cc_final: 0.5262 (m) REVERT: m 27 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6493 (pm20) REVERT: m 66 GLU cc_start: 0.6762 (pm20) cc_final: 0.6508 (pm20) REVERT: n 69 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7635 (tpp-160) REVERT: o 72 ASN cc_start: 0.7237 (p0) cc_final: 0.6295 (p0) REVERT: p 2 LEU cc_start: 0.7919 (tp) cc_final: 0.7385 (pt) REVERT: p 24 THR cc_start: 0.6867 (m) cc_final: 0.6436 (m) REVERT: r 40 THR cc_start: 0.6894 (m) cc_final: 0.6584 (p) REVERT: r 72 TRP cc_start: 0.7240 (m100) cc_final: 0.6246 (m100) REVERT: s 29 ASN cc_start: 0.8230 (t0) cc_final: 0.7377 (t0) REVERT: t 15 LEU cc_start: 0.8283 (tp) cc_final: 0.8047 (tt) REVERT: t 52 ASN cc_start: 0.6876 (p0) cc_final: 0.6348 (m110) REVERT: x 26 MET cc_start: 0.8231 (pmm) cc_final: 0.7382 (pmm) REVERT: x 31 ILE cc_start: 0.6374 (mt) cc_final: 0.6002 (mt) outliers start: 13 outliers final: 2 residues processed: 1864 average time/residue: 1.4342 time to fit residues: 4444.1686 Evaluate side-chains 1481 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1478 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 793 optimal weight: 6.9990 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 955 optimal weight: 8.9990 chunk 1031 optimal weight: 30.0000 chunk 850 optimal weight: 9.9990 chunk 947 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 766 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 3 GLN ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 225 ASN C 250 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN G 72 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 31 GLN S 60 HIS S 61 ASN T 70 HIS X 35 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 169 HIS d 202 ASN ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 GLN h 147 ASN ** i 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 4 GLN ** m 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 39 GLN p 45 HIS ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 63 GLN s 79 ASN t 51 HIS t 55 GLN u 73 HIS ** x 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 19 HIS ** x 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 60 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 159874 Z= 0.372 Angle : 0.824 19.474 238843 Z= 0.421 Chirality : 0.043 0.383 30483 Planarity : 0.007 0.116 13036 Dihedral : 23.275 179.867 79158 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.54 % Favored : 90.88 % Rotamer: Outliers : 0.26 % Allowed : 5.65 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.07 % 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: -2.54 (0.10), residues: 6020 helix: -1.02 (0.11), residues: 1767 sheet: -1.73 (0.14), residues: 1020 loop : -2.07 (0.10), residues: 3233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP J 15 HIS 0.015 0.003 HIS G 110 PHE 0.031 0.003 PHE O 97 TYR 0.035 0.003 TYR s 17 ARG 0.028 0.001 ARG i 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1767 time to evaluate : 6.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 ASP cc_start: 0.7015 (m-30) cc_final: 0.6814 (m-30) REVERT: 0 54 ILE cc_start: 0.8236 (mm) cc_final: 0.8018 (mm) REVERT: 1 29 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7767 (ttmt) REVERT: 1 39 ASP cc_start: 0.6846 (p0) cc_final: 0.6637 (p0) REVERT: 2 8 SER cc_start: 0.8723 (t) cc_final: 0.8395 (m) REVERT: 2 25 LYS cc_start: 0.9072 (pttm) cc_final: 0.8833 (ptpt) REVERT: 3 32 LEU cc_start: 0.6945 (mt) cc_final: 0.6739 (mt) REVERT: C 43 ASN cc_start: 0.8610 (p0) cc_final: 0.7902 (p0) REVERT: C 80 LEU cc_start: 0.8428 (mm) cc_final: 0.7960 (mt) REVERT: C 90 ILE cc_start: 0.8438 (pt) cc_final: 0.8081 (mp) REVERT: C 187 CYS cc_start: 0.7535 (m) cc_final: 0.6573 (m) REVERT: D 15 PHE cc_start: 0.6806 (m-80) cc_final: 0.6601 (m-10) REVERT: D 40 LEU cc_start: 0.8547 (mm) cc_final: 0.8346 (mm) REVERT: D 91 THR cc_start: 0.7893 (p) cc_final: 0.7430 (m) REVERT: D 103 ASP cc_start: 0.8089 (p0) cc_final: 0.7541 (p0) REVERT: D 149 ASN cc_start: 0.8962 (t0) cc_final: 0.8634 (t0) REVERT: D 175 LEU cc_start: 0.9072 (mt) cc_final: 0.8661 (mt) REVERT: D 188 LEU cc_start: 0.7526 (mm) cc_final: 0.7213 (mm) REVERT: E 1 MET cc_start: 0.5366 (ptm) cc_final: 0.3526 (ttm) REVERT: E 88 ARG cc_start: 0.7722 (mmp80) cc_final: 0.7425 (mmp80) REVERT: E 97 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6696 (t0) REVERT: E 132 LYS cc_start: 0.8608 (pttt) cc_final: 0.8295 (pttt) REVERT: E 197 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7136 (tp30) REVERT: F 28 PRO cc_start: 0.8883 (Cg_exo) cc_final: 0.8455 (Cg_endo) REVERT: F 29 ARG cc_start: 0.9038 (tpp-160) cc_final: 0.8575 (tpp-160) REVERT: F 48 LEU cc_start: 0.7807 (mp) cc_final: 0.7600 (mp) REVERT: F 56 LEU cc_start: 0.7825 (mt) cc_final: 0.7248 (tt) REVERT: F 95 MET cc_start: 0.8187 (ttp) cc_final: 0.6677 (ttt) REVERT: F 100 GLU cc_start: 0.7518 (tt0) cc_final: 0.7180 (tt0) REVERT: G 147 LEU cc_start: 0.8515 (mm) cc_final: 0.8283 (mm) REVERT: H 1 MET cc_start: 0.4576 (ptm) cc_final: 0.3595 (ptp) REVERT: I 135 MET cc_start: 0.1150 (tmm) cc_final: -0.0979 (mpp) REVERT: J 1 MET cc_start: 0.2634 (ttt) cc_final: 0.2230 (ttt) REVERT: J 114 LEU cc_start: 0.8705 (tp) cc_final: 0.7500 (tp) REVERT: K 6 THR cc_start: 0.6839 (p) cc_final: 0.6336 (p) REVERT: K 7 MET cc_start: 0.6745 (tpt) cc_final: 0.4491 (mtt) REVERT: K 8 LEU cc_start: 0.6947 (mp) cc_final: 0.6679 (mp) REVERT: K 40 LYS cc_start: 0.7375 (tptt) cc_final: 0.6698 (tttp) REVERT: L 3 LEU cc_start: 0.8725 (tp) cc_final: 0.8502 (tp) REVERT: L 135 ILE cc_start: 0.8121 (mt) cc_final: 0.7871 (mt) REVERT: M 31 PHE cc_start: 0.7745 (m-10) cc_final: 0.7121 (m-80) REVERT: N 1 MET cc_start: 0.7742 (mtm) cc_final: 0.7484 (mtm) REVERT: N 12 ARG cc_start: 0.7186 (mtt90) cc_final: 0.6933 (mmm160) REVERT: N 24 MET cc_start: 0.6849 (ttp) cc_final: 0.6398 (ttp) REVERT: N 44 LEU cc_start: 0.8726 (tp) cc_final: 0.8213 (tp) REVERT: O 40 ILE cc_start: 0.7206 (tp) cc_final: 0.6968 (tp) REVERT: O 98 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8240 (tm-30) REVERT: P 24 THR cc_start: 0.6542 (m) cc_final: 0.5998 (p) REVERT: P 74 GLN cc_start: 0.8396 (mp10) cc_final: 0.8012 (mp10) REVERT: P 102 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.7372 (tpp80) REVERT: P 110 LYS cc_start: 0.8250 (tmtt) cc_final: 0.7829 (ptpt) REVERT: Q 13 HIS cc_start: 0.7902 (m-70) cc_final: 0.7499 (m170) REVERT: Q 19 GLN cc_start: 0.7746 (mt0) cc_final: 0.7447 (mt0) REVERT: Q 23 TYR cc_start: 0.7799 (m-80) cc_final: 0.7385 (m-80) REVERT: Q 97 ILE cc_start: 0.6529 (mt) cc_final: 0.6250 (mt) REVERT: Q 108 LEU cc_start: 0.7959 (mm) cc_final: 0.7733 (mm) REVERT: R 14 VAL cc_start: 0.7689 (t) cc_final: 0.7370 (m) REVERT: S 84 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5946 (mmm-85) REVERT: S 94 ASP cc_start: 0.7896 (m-30) cc_final: 0.7683 (m-30) REVERT: T 19 LYS cc_start: 0.7723 (tttt) cc_final: 0.7421 (tttt) REVERT: T 22 THR cc_start: 0.8749 (p) cc_final: 0.8524 (m) REVERT: T 51 PHE cc_start: 0.7222 (m-80) cc_final: 0.6877 (m-80) REVERT: U 72 PHE cc_start: 0.6410 (t80) cc_final: 0.5942 (t80) REVERT: V 26 PHE cc_start: 0.7855 (p90) cc_final: 0.6940 (p90) REVERT: V 42 LEU cc_start: 0.5554 (mm) cc_final: 0.4715 (mm) REVERT: V 45 ASP cc_start: 0.8018 (m-30) cc_final: 0.7810 (t70) REVERT: W 15 LYS cc_start: 0.7320 (mtpt) cc_final: 0.7086 (mtmt) REVERT: X 50 VAL cc_start: 0.9212 (m) cc_final: 0.8837 (p) REVERT: Y 1 MET cc_start: 0.3998 (tpt) cc_final: 0.3687 (tpt) REVERT: Y 18 LEU cc_start: 0.8629 (mt) cc_final: 0.8311 (mt) REVERT: Y 28 LEU cc_start: 0.9002 (tp) cc_final: 0.8394 (tp) REVERT: Z 31 ILE cc_start: 0.9301 (mt) cc_final: 0.9060 (mt) REVERT: b 397 MET cc_start: 0.2710 (mpp) cc_final: 0.2198 (mpp) REVERT: b 514 LEU cc_start: 0.8546 (mt) cc_final: 0.8203 (mt) REVERT: b 583 THR cc_start: 0.4153 (p) cc_final: 0.3943 (p) REVERT: b 601 PHE cc_start: 0.7616 (p90) cc_final: 0.6870 (p90) REVERT: b 603 TYR cc_start: 0.7696 (p90) cc_final: 0.7343 (p90) REVERT: b 842 LEU cc_start: 0.6424 (tp) cc_final: 0.5633 (tp) REVERT: c 156 LEU cc_start: 0.6988 (mp) cc_final: 0.5648 (mp) REVERT: c 164 THR cc_start: 0.2430 (p) cc_final: 0.1717 (p) REVERT: c 165 GLU cc_start: 0.6290 (tt0) cc_final: 0.5674 (tt0) REVERT: d 45 THR cc_start: 0.6289 (t) cc_final: 0.5978 (t) REVERT: d 48 MET cc_start: 0.2929 (tmm) cc_final: 0.1973 (tpp) REVERT: d 153 MET cc_start: 0.7029 (mtt) cc_final: 0.6497 (mtt) REVERT: f 94 PHE cc_start: 0.6789 (t80) cc_final: 0.6121 (t80) REVERT: f 99 SER cc_start: 0.7433 (t) cc_final: 0.6888 (m) REVERT: f 137 ARG cc_start: 0.8316 (mtm180) cc_final: 0.8073 (mtm180) REVERT: g 54 LEU cc_start: 0.9019 (mp) cc_final: 0.8007 (mt) REVERT: g 63 ILE cc_start: 0.7649 (mm) cc_final: 0.7439 (mm) REVERT: g 89 LEU cc_start: 0.8519 (tp) cc_final: 0.7806 (tp) REVERT: g 125 ASN cc_start: 0.7566 (m-40) cc_final: 0.6722 (t0) REVERT: g 141 VAL cc_start: 0.7740 (m) cc_final: 0.7070 (t) REVERT: g 149 LYS cc_start: 0.7732 (tptt) cc_final: 0.7387 (tptt) REVERT: h 140 VAL cc_start: 0.0840 (t) cc_final: 0.0607 (t) REVERT: h 143 MET cc_start: 0.4284 (tmm) cc_final: 0.3824 (ppp) REVERT: i 1 MET cc_start: 0.1864 (tpp) cc_final: 0.1401 (tpp) REVERT: j 78 ILE cc_start: 0.8377 (mm) cc_final: 0.8141 (mm) REVERT: j 87 MET cc_start: 0.7062 (mmm) cc_final: 0.6611 (mmm) REVERT: k 86 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7362 (mmmm) REVERT: k 95 MET cc_start: 0.7420 (mtt) cc_final: 0.7163 (mtt) REVERT: k 110 MET cc_start: 0.5047 (pmm) cc_final: 0.4823 (pmm) REVERT: m 72 ARG cc_start: 0.7186 (mmt-90) cc_final: 0.6953 (mmp80) REVERT: o 72 ASN cc_start: 0.7855 (p0) cc_final: 0.7455 (m-40) REVERT: p 2 LEU cc_start: 0.8209 (tp) cc_final: 0.7916 (pt) REVERT: p 23 SER cc_start: 0.8143 (t) cc_final: 0.7773 (m) REVERT: p 69 LEU cc_start: 0.8120 (mm) cc_final: 0.7738 (mm) REVERT: p 76 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7992 (ttm-80) REVERT: q 79 LEU cc_start: 0.7826 (mt) cc_final: 0.7203 (mp) REVERT: r 20 ILE cc_start: 0.7792 (mt) cc_final: 0.7283 (mt) REVERT: r 72 TRP cc_start: 0.7739 (m100) cc_final: 0.7333 (m100) REVERT: s 21 VAL cc_start: 0.8155 (t) cc_final: 0.7711 (t) REVERT: s 29 ASN cc_start: 0.8135 (t0) cc_final: 0.7807 (t0) REVERT: u 32 ILE cc_start: 0.6883 (mt) cc_final: 0.6635 (mt) REVERT: x 26 MET cc_start: 0.7755 (pmm) cc_final: 0.7138 (pmm) outliers start: 13 outliers final: 5 residues processed: 1775 average time/residue: 1.4325 time to fit residues: 4232.9434 Evaluate side-chains 1480 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1474 time to evaluate : 6.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 5.9990 chunk 718 optimal weight: 30.0000 chunk 495 optimal weight: 0.0040 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 641 optimal weight: 20.0000 chunk 958 optimal weight: 0.0170 chunk 1014 optimal weight: 2.9990 chunk 500 optimal weight: 5.9990 chunk 908 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN 2 16 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 133 ASN D 32 ASN D 67 HIS ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN N 3 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN R 66 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 HIS Y 27 ASN Z 33 HIS ** b 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 592 HIS b 670 GLN c 2 GLN ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN c 138 GLN ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 141 HIS ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS k 117 GLN o 19 ASN r 44 HIS ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS x 19 HIS ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 159874 Z= 0.185 Angle : 0.614 19.155 238843 Z= 0.320 Chirality : 0.034 0.298 30483 Planarity : 0.006 0.290 13036 Dihedral : 23.196 179.338 79158 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.16 % Favored : 92.26 % Rotamer: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 6020 helix: -0.53 (0.12), residues: 1771 sheet: -1.43 (0.14), residues: 1048 loop : -1.95 (0.10), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 15 HIS 0.012 0.001 HIS J 80 PHE 0.024 0.002 PHE g 106 TYR 0.021 0.002 TYR g 50 ARG 0.019 0.001 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1715 time to evaluate : 5.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 43 THR cc_start: 0.7707 (p) cc_final: 0.7493 (p) REVERT: 1 29 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7753 (ttmt) REVERT: 1 43 ARG cc_start: 0.7468 (mmm160) cc_final: 0.6084 (mtp180) REVERT: 2 22 MET cc_start: 0.7875 (tpt) cc_final: 0.7355 (tpt) REVERT: 2 25 LYS cc_start: 0.9009 (pttm) cc_final: 0.8726 (ptpp) REVERT: 3 32 LEU cc_start: 0.7306 (mt) cc_final: 0.7085 (mt) REVERT: 4 9 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7766 (mmtt) REVERT: 4 16 ILE cc_start: 0.8981 (mt) cc_final: 0.8540 (mt) REVERT: C 80 LEU cc_start: 0.8450 (mm) cc_final: 0.8035 (mm) REVERT: C 187 CYS cc_start: 0.7538 (m) cc_final: 0.6576 (m) REVERT: C 212 TRP cc_start: 0.8395 (p90) cc_final: 0.7956 (p90) REVERT: C 231 HIS cc_start: 0.7512 (m170) cc_final: 0.7052 (m170) REVERT: C 239 PHE cc_start: 0.8386 (t80) cc_final: 0.8098 (t80) REVERT: D 15 PHE cc_start: 0.6994 (m-80) cc_final: 0.6567 (m-10) REVERT: D 43 ASP cc_start: 0.7371 (p0) cc_final: 0.6273 (t0) REVERT: D 51 THR cc_start: 0.7283 (t) cc_final: 0.7077 (t) REVERT: D 91 THR cc_start: 0.7921 (p) cc_final: 0.7532 (m) REVERT: D 123 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7902 (tptp) REVERT: D 149 ASN cc_start: 0.8568 (t0) cc_final: 0.8246 (t0) REVERT: D 169 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7742 (ttt180) REVERT: D 175 LEU cc_start: 0.8816 (mt) cc_final: 0.8248 (mt) REVERT: E 1 MET cc_start: 0.5071 (ptm) cc_final: 0.3290 (ttm) REVERT: E 85 PHE cc_start: 0.8085 (m-80) cc_final: 0.7884 (m-80) REVERT: E 88 ARG cc_start: 0.8051 (mmp80) cc_final: 0.7589 (mmp80) REVERT: E 132 LYS cc_start: 0.8409 (pttt) cc_final: 0.8077 (pttt) REVERT: E 197 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7006 (tp30) REVERT: F 95 MET cc_start: 0.8356 (ttp) cc_final: 0.7159 (ttp) REVERT: G 24 THR cc_start: 0.5404 (m) cc_final: 0.4850 (p) REVERT: G 72 ASN cc_start: 0.7310 (m-40) cc_final: 0.7016 (m110) REVERT: G 86 LEU cc_start: 0.7189 (mm) cc_final: 0.6687 (mm) REVERT: H 1 MET cc_start: 0.4869 (ptm) cc_final: 0.4569 (ppp) REVERT: I 135 MET cc_start: 0.2339 (tmm) cc_final: -0.0608 (mpp) REVERT: J 1 MET cc_start: 0.2524 (ttt) cc_final: 0.2075 (ttt) REVERT: J 52 ASP cc_start: 0.7005 (m-30) cc_final: 0.6489 (m-30) REVERT: J 109 LEU cc_start: 0.9093 (mt) cc_final: 0.8795 (tp) REVERT: J 114 LEU cc_start: 0.8330 (tp) cc_final: 0.7250 (tp) REVERT: K 6 THR cc_start: 0.6479 (p) cc_final: 0.6085 (p) REVERT: K 7 MET cc_start: 0.6720 (tpt) cc_final: 0.4621 (mtm) REVERT: K 23 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7550 (mtpt) REVERT: L 3 LEU cc_start: 0.8787 (tp) cc_final: 0.8554 (tp) REVERT: L 135 ILE cc_start: 0.8221 (mt) cc_final: 0.8017 (mt) REVERT: M 31 PHE cc_start: 0.7670 (m-10) cc_final: 0.7439 (m-80) REVERT: N 1 MET cc_start: 0.7770 (mtm) cc_final: 0.7413 (mtm) REVERT: N 24 MET cc_start: 0.7139 (ttp) cc_final: 0.6444 (ttp) REVERT: N 34 ILE cc_start: 0.7675 (pt) cc_final: 0.7455 (pt) REVERT: N 44 LEU cc_start: 0.8797 (tp) cc_final: 0.8376 (tp) REVERT: N 114 GLU cc_start: 0.6410 (pp20) cc_final: 0.6194 (pp20) REVERT: O 39 VAL cc_start: 0.7907 (t) cc_final: 0.7637 (t) REVERT: O 76 LYS cc_start: 0.7424 (ptpp) cc_final: 0.7069 (pttm) REVERT: O 92 PHE cc_start: 0.7452 (t80) cc_final: 0.7066 (t80) REVERT: P 6 GLN cc_start: 0.7235 (pt0) cc_final: 0.6907 (pt0) REVERT: P 24 THR cc_start: 0.6545 (m) cc_final: 0.6187 (p) REVERT: P 27 VAL cc_start: 0.8097 (t) cc_final: 0.7780 (t) REVERT: P 102 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.7353 (tpp80) REVERT: Q 13 HIS cc_start: 0.7838 (m-70) cc_final: 0.7556 (m-70) REVERT: Q 23 TYR cc_start: 0.7766 (m-80) cc_final: 0.7392 (m-80) REVERT: Q 51 GLN cc_start: 0.7311 (mt0) cc_final: 0.7043 (mt0) REVERT: Q 57 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7683 (tpp80) REVERT: Q 93 ILE cc_start: 0.9159 (mm) cc_final: 0.8856 (mm) REVERT: Q 97 ILE cc_start: 0.6983 (mt) cc_final: 0.6528 (mt) REVERT: Q 99 VAL cc_start: 0.8857 (t) cc_final: 0.8596 (t) REVERT: R 14 VAL cc_start: 0.7648 (t) cc_final: 0.7016 (m) REVERT: T 3 ARG cc_start: 0.4956 (ttm110) cc_final: 0.4523 (tpt-90) REVERT: T 10 VAL cc_start: 0.8721 (t) cc_final: 0.8455 (p) REVERT: T 19 LYS cc_start: 0.7474 (tttt) cc_final: 0.7098 (ttpt) REVERT: V 26 PHE cc_start: 0.7716 (p90) cc_final: 0.7459 (p90) REVERT: V 42 LEU cc_start: 0.6331 (mm) cc_final: 0.5814 (mm) REVERT: W 55 LEU cc_start: 0.7730 (mm) cc_final: 0.7522 (mm) REVERT: X 28 PHE cc_start: 0.7439 (m-80) cc_final: 0.7150 (m-10) REVERT: Y 1 MET cc_start: 0.4348 (tpt) cc_final: 0.3641 (tpt) REVERT: Z 31 ILE cc_start: 0.9253 (mt) cc_final: 0.9007 (mt) REVERT: Z 52 PHE cc_start: 0.7160 (p90) cc_final: 0.6830 (p90) REVERT: b 397 MET cc_start: 0.2813 (mpp) cc_final: 0.2563 (mpp) REVERT: b 509 ARG cc_start: 0.8573 (ptm160) cc_final: 0.7984 (ptm-80) REVERT: b 583 THR cc_start: 0.4083 (p) cc_final: 0.3800 (p) REVERT: b 691 ILE cc_start: 0.8154 (pt) cc_final: 0.7923 (pt) REVERT: b 822 VAL cc_start: 0.8756 (p) cc_final: 0.8546 (p) REVERT: b 859 MET cc_start: 0.6645 (tmm) cc_final: 0.6373 (tmm) REVERT: b 867 ASN cc_start: 0.7507 (t0) cc_final: 0.6592 (t0) REVERT: c 13 ILE cc_start: 0.6840 (mp) cc_final: 0.6491 (tp) REVERT: c 131 ARG cc_start: 0.7365 (ptt180) cc_final: 0.6955 (ptt90) REVERT: c 183 TYR cc_start: 0.7966 (t80) cc_final: 0.7701 (t80) REVERT: d 116 LEU cc_start: 0.7101 (tp) cc_final: 0.6713 (tt) REVERT: d 153 MET cc_start: 0.6686 (mtt) cc_final: 0.6278 (mtt) REVERT: f 94 PHE cc_start: 0.6973 (t80) cc_final: 0.6491 (t80) REVERT: f 99 SER cc_start: 0.7585 (t) cc_final: 0.7038 (m) REVERT: g 54 LEU cc_start: 0.8957 (mp) cc_final: 0.8074 (mt) REVERT: g 88 ASN cc_start: 0.7743 (m-40) cc_final: 0.7486 (m-40) REVERT: g 89 LEU cc_start: 0.8499 (tp) cc_final: 0.7576 (tp) REVERT: g 98 ASP cc_start: 0.7451 (p0) cc_final: 0.7145 (p0) REVERT: g 104 MET cc_start: 0.7313 (tmm) cc_final: 0.6905 (tmm) REVERT: g 114 ARG cc_start: 0.5403 (ttm110) cc_final: 0.5017 (ttm110) REVERT: g 125 ASN cc_start: 0.7384 (m-40) cc_final: 0.6575 (t0) REVERT: g 149 LYS cc_start: 0.7405 (tptt) cc_final: 0.6939 (tptt) REVERT: h 100 MET cc_start: 0.4643 (mtp) cc_final: 0.3860 (ttm) REVERT: h 143 MET cc_start: 0.5448 (tmm) cc_final: 0.5014 (ppp) REVERT: i 1 MET cc_start: 0.1802 (tpp) cc_final: 0.1128 (tpp) REVERT: i 23 GLU cc_start: 0.8741 (pp20) cc_final: 0.8491 (pm20) REVERT: k 49 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7813 (ptpp) REVERT: k 83 ARG cc_start: 0.8427 (mmt90) cc_final: 0.8090 (mmt-90) REVERT: k 84 ILE cc_start: 0.8427 (mp) cc_final: 0.7802 (mp) REVERT: m 88 MET cc_start: 0.4156 (mtp) cc_final: 0.3875 (mtm) REVERT: o 72 ASN cc_start: 0.7767 (p0) cc_final: 0.7529 (m-40) REVERT: p 23 SER cc_start: 0.8328 (t) cc_final: 0.7977 (m) REVERT: p 26 VAL cc_start: 0.5974 (t) cc_final: 0.5705 (t) REVERT: p 53 ARG cc_start: 0.8043 (mtp85) cc_final: 0.6854 (ttm-80) REVERT: q 10 VAL cc_start: 0.8926 (t) cc_final: 0.8651 (t) REVERT: q 19 TYR cc_start: 0.6379 (m-80) cc_final: 0.6058 (m-80) REVERT: r 27 PHE cc_start: 0.7110 (m-80) cc_final: 0.6694 (m-80) REVERT: r 44 HIS cc_start: 0.6469 (m90) cc_final: 0.6268 (m90) REVERT: r 72 TRP cc_start: 0.7607 (m100) cc_final: 0.7345 (m100) REVERT: s 29 ASN cc_start: 0.8043 (t0) cc_final: 0.7680 (t0) REVERT: t 52 ASN cc_start: 0.6605 (p0) cc_final: 0.5927 (m-40) REVERT: u 58 ILE cc_start: 0.8126 (mt) cc_final: 0.7896 (mp) REVERT: u 62 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: w 46 ARG cc_start: 0.7163 (mmp80) cc_final: 0.6811 (mmp80) REVERT: x 26 MET cc_start: 0.7741 (pmm) cc_final: 0.6873 (pmm) REVERT: x 31 ILE cc_start: 0.6952 (mt) cc_final: 0.6504 (mt) REVERT: x 57 VAL cc_start: 0.8639 (m) cc_final: 0.8329 (m) outliers start: 4 outliers final: 1 residues processed: 1715 average time/residue: 1.4059 time to fit residues: 4045.8781 Evaluate side-chains 1473 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1472 time to evaluate : 6.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 9.9990 chunk 576 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 755 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 866 optimal weight: 1.9990 chunk 701 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 518 optimal weight: 0.9980 chunk 910 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN 0 5 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 164 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 18 GLN R 66 HIS S 7 HIS S 31 GLN S 61 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN U 65 GLN Y 27 ASN Y 31 GLN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** b 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN ** f 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 11 HIS ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 27 GLN ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 18 GLN x 19 HIS x 47 GLN x 54 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 159874 Z= 0.203 Angle : 0.617 17.917 238843 Z= 0.320 Chirality : 0.034 0.348 30483 Planarity : 0.006 0.167 13036 Dihedral : 23.212 179.004 79158 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.12 % Favored : 91.33 % Rotamer: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 6020 helix: -0.36 (0.12), residues: 1760 sheet: -1.33 (0.14), residues: 1068 loop : -1.89 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP s 60 HIS 0.012 0.002 HIS J 80 PHE 0.030 0.002 PHE M 117 TYR 0.018 0.002 TYR g 50 ARG 0.027 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1698 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1695 time to evaluate : 6.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 53 VAL cc_start: 0.8900 (m) cc_final: 0.8555 (m) REVERT: 0 54 ILE cc_start: 0.8081 (mp) cc_final: 0.7873 (mp) REVERT: 1 29 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7735 (ttmt) REVERT: 2 29 GLN cc_start: 0.7744 (tp40) cc_final: 0.7501 (mm-40) REVERT: 2 33 ARG cc_start: 0.9049 (ptt90) cc_final: 0.8754 (ptt180) REVERT: 3 3 ILE cc_start: 0.8854 (mt) cc_final: 0.8573 (mt) REVERT: 3 32 LEU cc_start: 0.7299 (mt) cc_final: 0.7057 (mt) REVERT: 3 63 TYR cc_start: 0.7024 (m-80) cc_final: 0.6664 (m-80) REVERT: C 51 ARG cc_start: 0.7313 (ptt-90) cc_final: 0.7065 (ptt-90) REVERT: C 115 ILE cc_start: 0.8008 (tt) cc_final: 0.7719 (tt) REVERT: C 184 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6460 (mm-30) REVERT: C 187 CYS cc_start: 0.7508 (m) cc_final: 0.6231 (m) REVERT: C 200 MET cc_start: 0.7372 (tpt) cc_final: 0.6854 (tpt) REVERT: C 206 LYS cc_start: 0.8434 (tttm) cc_final: 0.8215 (tttm) REVERT: C 231 HIS cc_start: 0.7508 (m170) cc_final: 0.7071 (m170) REVERT: C 256 THR cc_start: 0.7069 (p) cc_final: 0.6623 (t) REVERT: D 43 ASP cc_start: 0.7372 (p0) cc_final: 0.6291 (t0) REVERT: D 91 THR cc_start: 0.8015 (p) cc_final: 0.7595 (m) REVERT: D 103 ASP cc_start: 0.7646 (p0) cc_final: 0.7343 (p0) REVERT: D 149 ASN cc_start: 0.8396 (t0) cc_final: 0.8184 (t0) REVERT: D 189 VAL cc_start: 0.8720 (m) cc_final: 0.8505 (p) REVERT: E 1 MET cc_start: 0.5123 (ptm) cc_final: 0.3279 (ttm) REVERT: E 88 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7518 (mmp80) REVERT: E 100 MET cc_start: 0.7991 (mtm) cc_final: 0.7767 (mtt) REVERT: E 197 GLU cc_start: 0.7762 (mm-30) cc_final: 0.6720 (tp30) REVERT: F 25 MET cc_start: 0.4305 (ttm) cc_final: 0.4064 (ttm) REVERT: F 48 LEU cc_start: 0.7888 (mp) cc_final: 0.7665 (mp) REVERT: F 95 MET cc_start: 0.8310 (ttp) cc_final: 0.7848 (ttp) REVERT: F 100 GLU cc_start: 0.7234 (tt0) cc_final: 0.6920 (tt0) REVERT: G 24 THR cc_start: 0.5295 (m) cc_final: 0.4878 (p) REVERT: H 1 MET cc_start: 0.4709 (ptm) cc_final: 0.4071 (ptp) REVERT: I 135 MET cc_start: 0.3207 (tmm) cc_final: 0.0718 (mpp) REVERT: J 44 TYR cc_start: 0.8045 (t80) cc_final: 0.7691 (t80) REVERT: J 45 THR cc_start: 0.9036 (m) cc_final: 0.8437 (m) REVERT: J 54 ILE cc_start: 0.7234 (mt) cc_final: 0.6590 (mt) REVERT: J 98 GLU cc_start: 0.7723 (mp0) cc_final: 0.7496 (mp0) REVERT: J 109 LEU cc_start: 0.8641 (mt) cc_final: 0.8222 (tp) REVERT: J 114 LEU cc_start: 0.8305 (tp) cc_final: 0.7304 (tp) REVERT: K 6 THR cc_start: 0.6408 (p) cc_final: 0.5893 (p) REVERT: K 7 MET cc_start: 0.7393 (tpt) cc_final: 0.5736 (mtm) REVERT: K 8 LEU cc_start: 0.6783 (mp) cc_final: 0.6558 (mp) REVERT: K 23 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7569 (mtpt) REVERT: K 40 LYS cc_start: 0.7440 (tptt) cc_final: 0.6881 (tppt) REVERT: L 78 ARG cc_start: 0.8143 (mpt-90) cc_final: 0.7817 (mtt-85) REVERT: L 135 ILE cc_start: 0.8258 (mt) cc_final: 0.8032 (mt) REVERT: M 31 PHE cc_start: 0.7481 (m-80) cc_final: 0.7227 (m-80) REVERT: N 1 MET cc_start: 0.7590 (mtm) cc_final: 0.7323 (mtm) REVERT: N 24 MET cc_start: 0.6952 (ttp) cc_final: 0.6422 (ttp) REVERT: N 44 LEU cc_start: 0.8715 (tp) cc_final: 0.8111 (tp) REVERT: N 114 GLU cc_start: 0.6217 (pp20) cc_final: 0.6010 (pp20) REVERT: O 31 THR cc_start: 0.4674 (m) cc_final: 0.3734 (m) REVERT: O 39 VAL cc_start: 0.8156 (t) cc_final: 0.7751 (t) REVERT: O 49 VAL cc_start: 0.8852 (t) cc_final: 0.8469 (p) REVERT: O 76 LYS cc_start: 0.7318 (ptpp) cc_final: 0.7054 (pttm) REVERT: O 102 ARG cc_start: 0.7010 (mtm180) cc_final: 0.5710 (mtt180) REVERT: P 24 THR cc_start: 0.6619 (m) cc_final: 0.6241 (p) REVERT: P 74 GLN cc_start: 0.7697 (mp10) cc_final: 0.7249 (mp10) REVERT: Q 13 HIS cc_start: 0.7964 (m-70) cc_final: 0.7671 (m-70) REVERT: Q 14 LYS cc_start: 0.8681 (tppp) cc_final: 0.8428 (mmtt) REVERT: Q 23 TYR cc_start: 0.7923 (m-80) cc_final: 0.7554 (m-80) REVERT: Q 47 ARG cc_start: 0.5593 (ttp-170) cc_final: 0.4895 (ttp-170) REVERT: Q 63 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7321 (mtt180) REVERT: Q 97 ILE cc_start: 0.7060 (mt) cc_final: 0.6548 (mt) REVERT: Q 99 VAL cc_start: 0.8818 (t) cc_final: 0.8618 (t) REVERT: T 3 ARG cc_start: 0.4962 (ttm110) cc_final: 0.4583 (tpt-90) REVERT: U 35 VAL cc_start: 0.7400 (p) cc_final: 0.7033 (p) REVERT: U 65 GLN cc_start: 0.7796 (mt0) cc_final: 0.7445 (mt0) REVERT: V 26 PHE cc_start: 0.7774 (p90) cc_final: 0.7534 (p90) REVERT: W 55 LEU cc_start: 0.7635 (mm) cc_final: 0.7431 (mm) REVERT: Y 1 MET cc_start: 0.4583 (tpt) cc_final: 0.4008 (tpt) REVERT: Y 47 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7171 (ttp-110) REVERT: Z 37 ARG cc_start: 0.7407 (mmp-170) cc_final: 0.7048 (mmp-170) REVERT: Z 50 VAL cc_start: 0.6548 (t) cc_final: 0.6100 (t) REVERT: Z 52 PHE cc_start: 0.7214 (p90) cc_final: 0.6702 (p90) REVERT: Z 53 MET cc_start: 0.8058 (tmm) cc_final: 0.7461 (ppp) REVERT: b 509 ARG cc_start: 0.8646 (ptm160) cc_final: 0.8251 (ptm-80) REVERT: b 583 THR cc_start: 0.4016 (p) cc_final: 0.3749 (p) REVERT: b 601 PHE cc_start: 0.7303 (p90) cc_final: 0.6475 (p90) REVERT: b 729 THR cc_start: 0.6848 (p) cc_final: 0.6517 (p) REVERT: b 732 ASP cc_start: 0.8668 (t0) cc_final: 0.8242 (m-30) REVERT: b 816 MET cc_start: 0.7169 (tpt) cc_final: 0.6850 (tpt) REVERT: b 859 MET cc_start: 0.6721 (tmm) cc_final: 0.6280 (tmm) REVERT: b 867 ASN cc_start: 0.8062 (t0) cc_final: 0.7223 (t0) REVERT: c 13 ILE cc_start: 0.6736 (mp) cc_final: 0.6449 (tp) REVERT: c 42 LEU cc_start: 0.6465 (tt) cc_final: 0.6106 (tp) REVERT: c 168 ARG cc_start: 0.7322 (tmm160) cc_final: 0.7103 (tmm160) REVERT: d 27 LYS cc_start: 0.6806 (tmmt) cc_final: 0.4597 (tppt) REVERT: d 153 MET cc_start: 0.7006 (mtt) cc_final: 0.6510 (mtt) REVERT: f 94 PHE cc_start: 0.6900 (t80) cc_final: 0.6371 (t80) REVERT: f 99 SER cc_start: 0.7670 (t) cc_final: 0.7146 (m) REVERT: g 28 ASP cc_start: 0.6618 (m-30) cc_final: 0.6414 (m-30) REVERT: g 54 LEU cc_start: 0.8916 (mp) cc_final: 0.8076 (mt) REVERT: g 89 LEU cc_start: 0.8594 (tp) cc_final: 0.7811 (tp) REVERT: g 98 ASP cc_start: 0.7319 (p0) cc_final: 0.7054 (p0) REVERT: g 114 ARG cc_start: 0.5593 (ttm110) cc_final: 0.5252 (ttm110) REVERT: g 125 ASN cc_start: 0.7429 (m-40) cc_final: 0.6608 (t0) REVERT: g 149 LYS cc_start: 0.7819 (tptt) cc_final: 0.7254 (tptt) REVERT: h 143 MET cc_start: 0.5028 (tmm) cc_final: 0.4687 (ppp) REVERT: i 1 MET cc_start: 0.1678 (tpp) cc_final: 0.1431 (tpp) REVERT: i 23 GLU cc_start: 0.8711 (pp20) cc_final: 0.8479 (pm20) REVERT: k 82 LEU cc_start: 0.8608 (tt) cc_final: 0.8397 (tt) REVERT: m 88 MET cc_start: 0.4104 (mtp) cc_final: 0.3785 (mtm) REVERT: p 23 SER cc_start: 0.8277 (t) cc_final: 0.7841 (m) REVERT: q 67 THR cc_start: 0.7152 (p) cc_final: 0.6925 (p) REVERT: s 21 VAL cc_start: 0.7915 (t) cc_final: 0.7612 (t) REVERT: s 29 ASN cc_start: 0.7954 (t0) cc_final: 0.7690 (t0) REVERT: t 52 ASN cc_start: 0.6283 (p0) cc_final: 0.6004 (m-40) REVERT: x 26 MET cc_start: 0.7828 (pmm) cc_final: 0.6980 (pmm) REVERT: x 31 ILE cc_start: 0.7331 (mt) cc_final: 0.7050 (mt) outliers start: 3 outliers final: 2 residues processed: 1697 average time/residue: 1.3885 time to fit residues: 3955.5757 Evaluate side-chains 1456 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1454 time to evaluate : 6.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 7.9990 chunk 913 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 595 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 1015 optimal weight: 9.9990 chunk 843 optimal weight: 30.0000 chunk 470 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 533 optimal weight: 9.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 49 GLN D 140 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 74 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN b 592 HIS ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 189 HIS d 14 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 GLN g 151 GLN ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 39 GLN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS x 19 HIS ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 159874 Z= 0.312 Angle : 0.761 16.766 238843 Z= 0.391 Chirality : 0.040 0.320 30483 Planarity : 0.007 0.155 13036 Dihedral : 23.633 179.839 79158 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.52 % Favored : 89.93 % Rotamer: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.35 (0.10), residues: 6020 helix: -0.80 (0.11), residues: 1786 sheet: -1.38 (0.15), residues: 1008 loop : -2.08 (0.10), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP i 42 HIS 0.014 0.002 HIS J 80 PHE 0.028 0.003 PHE F 176 TYR 0.031 0.003 TYR c 183 ARG 0.017 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1686 time to evaluate : 6.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 32 THR cc_start: 0.7251 (p) cc_final: 0.7029 (p) REVERT: 1 29 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7877 (ttpt) REVERT: 1 43 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7004 (mtp180) REVERT: 1 45 HIS cc_start: 0.6041 (m90) cc_final: 0.5540 (m-70) REVERT: 2 8 SER cc_start: 0.8836 (t) cc_final: 0.8297 (m) REVERT: 2 9 VAL cc_start: 0.8121 (t) cc_final: 0.7900 (t) REVERT: 2 24 THR cc_start: 0.8374 (m) cc_final: 0.8131 (m) REVERT: 2 30 VAL cc_start: 0.9322 (t) cc_final: 0.8956 (t) REVERT: 3 32 LEU cc_start: 0.7597 (mt) cc_final: 0.7287 (mt) REVERT: 3 63 TYR cc_start: 0.7301 (m-80) cc_final: 0.6621 (m-80) REVERT: C 128 THR cc_start: 0.8199 (m) cc_final: 0.7777 (m) REVERT: C 184 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6501 (mm-30) REVERT: C 187 CYS cc_start: 0.7225 (m) cc_final: 0.6165 (m) REVERT: C 200 MET cc_start: 0.7367 (tpt) cc_final: 0.6812 (tpt) REVERT: C 206 LYS cc_start: 0.8482 (tttm) cc_final: 0.7931 (tttm) REVERT: D 149 ASN cc_start: 0.8882 (t0) cc_final: 0.8600 (t0) REVERT: D 189 VAL cc_start: 0.8485 (m) cc_final: 0.8284 (p) REVERT: E 1 MET cc_start: 0.5151 (ptm) cc_final: 0.3484 (ttm) REVERT: E 88 ARG cc_start: 0.7970 (mmp80) cc_final: 0.7553 (mmp80) REVERT: E 98 LYS cc_start: 0.8195 (mttt) cc_final: 0.7823 (mttt) REVERT: E 100 MET cc_start: 0.8314 (mtm) cc_final: 0.7603 (mtt) REVERT: F 25 MET cc_start: 0.4609 (ttm) cc_final: 0.4115 (ttm) REVERT: F 48 LEU cc_start: 0.8120 (mp) cc_final: 0.7911 (mp) REVERT: F 65 LEU cc_start: 0.6886 (tp) cc_final: 0.6643 (tp) REVERT: F 95 MET cc_start: 0.8617 (ttp) cc_final: 0.8136 (ttp) REVERT: F 100 GLU cc_start: 0.7261 (tt0) cc_final: 0.7050 (tt0) REVERT: G 24 THR cc_start: 0.5516 (m) cc_final: 0.5233 (p) REVERT: H 1 MET cc_start: 0.4680 (ptm) cc_final: 0.4312 (ptp) REVERT: I 135 MET cc_start: 0.4029 (tmm) cc_final: 0.1354 (mpp) REVERT: J 36 LEU cc_start: 0.7947 (mt) cc_final: 0.7217 (mt) REVERT: J 45 THR cc_start: 0.8957 (m) cc_final: 0.8291 (m) REVERT: J 54 ILE cc_start: 0.7541 (mt) cc_final: 0.6837 (mt) REVERT: J 77 HIS cc_start: 0.7170 (t-170) cc_final: 0.6662 (t-170) REVERT: J 114 LEU cc_start: 0.8362 (tp) cc_final: 0.7747 (tp) REVERT: K 6 THR cc_start: 0.6517 (p) cc_final: 0.5815 (p) REVERT: K 7 MET cc_start: 0.7018 (tpt) cc_final: 0.5846 (mtm) REVERT: K 8 LEU cc_start: 0.6967 (mp) cc_final: 0.6469 (mp) REVERT: K 40 LYS cc_start: 0.7565 (tptt) cc_final: 0.7301 (tttp) REVERT: K 70 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7005 (ttm110) REVERT: K 116 ILE cc_start: 0.8608 (pt) cc_final: 0.8345 (tp) REVERT: L 36 LYS cc_start: 0.6836 (mttt) cc_final: 0.6446 (mttt) REVERT: L 70 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7253 (mmmm) REVERT: L 78 ARG cc_start: 0.8200 (mpt-90) cc_final: 0.6999 (mtt180) REVERT: L 135 ILE cc_start: 0.8296 (mt) cc_final: 0.8044 (mt) REVERT: M 31 PHE cc_start: 0.7765 (m-80) cc_final: 0.7470 (m-80) REVERT: N 1 MET cc_start: 0.7876 (mtm) cc_final: 0.7139 (mtm) REVERT: N 40 LYS cc_start: 0.8500 (mttt) cc_final: 0.8251 (mttm) REVERT: N 44 LEU cc_start: 0.8744 (tp) cc_final: 0.8404 (tp) REVERT: N 114 GLU cc_start: 0.6146 (pp20) cc_final: 0.5729 (pp20) REVERT: O 31 THR cc_start: 0.4652 (m) cc_final: 0.3834 (m) REVERT: O 76 LYS cc_start: 0.7561 (ptpp) cc_final: 0.7258 (pttm) REVERT: O 102 ARG cc_start: 0.6963 (mtm180) cc_final: 0.5727 (mtt180) REVERT: P 74 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: P 102 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7540 (tpp-160) REVERT: Q 13 HIS cc_start: 0.7988 (m-70) cc_final: 0.7674 (m170) REVERT: Q 23 TYR cc_start: 0.7949 (m-80) cc_final: 0.7633 (m-80) REVERT: Q 51 GLN cc_start: 0.6852 (mt0) cc_final: 0.6471 (mt0) REVERT: Q 63 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7464 (mtt180) REVERT: Q 93 ILE cc_start: 0.9115 (mm) cc_final: 0.8836 (mm) REVERT: R 49 ILE cc_start: 0.4071 (pt) cc_final: 0.3869 (pt) REVERT: T 2 ILE cc_start: 0.8719 (mm) cc_final: 0.8376 (mt) REVERT: U 10 VAL cc_start: 0.7928 (p) cc_final: 0.7704 (p) REVERT: V 31 TYR cc_start: 0.6545 (p90) cc_final: 0.6339 (p90) REVERT: V 46 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7635 (mmmt) REVERT: V 92 VAL cc_start: 0.8947 (m) cc_final: 0.8699 (t) REVERT: W 55 LEU cc_start: 0.7780 (mm) cc_final: 0.7564 (mm) REVERT: X 9 LYS cc_start: 0.7432 (mptt) cc_final: 0.6878 (mmtp) REVERT: Y 1 MET cc_start: 0.3956 (tpt) cc_final: 0.3355 (tpt) REVERT: Y 27 ASN cc_start: 0.7654 (m-40) cc_final: 0.7197 (m-40) REVERT: Z 37 ARG cc_start: 0.7516 (mmp-170) cc_final: 0.7023 (mmp-170) REVERT: b 436 GLU cc_start: 0.8284 (pt0) cc_final: 0.7667 (pm20) REVERT: b 453 SER cc_start: 0.7803 (m) cc_final: 0.7407 (t) REVERT: b 509 ARG cc_start: 0.8684 (ptm160) cc_final: 0.7954 (ptm-80) REVERT: b 732 ASP cc_start: 0.8535 (t0) cc_final: 0.8197 (m-30) REVERT: b 859 MET cc_start: 0.6916 (tmm) cc_final: 0.6252 (tmm) REVERT: c 13 ILE cc_start: 0.6564 (mp) cc_final: 0.6266 (tp) REVERT: c 42 LEU cc_start: 0.6267 (tt) cc_final: 0.5843 (tp) REVERT: d 67 LEU cc_start: 0.8201 (tt) cc_final: 0.7997 (tt) REVERT: d 136 ARG cc_start: 0.3815 (ptt90) cc_final: 0.3580 (ptt90) REVERT: d 153 MET cc_start: 0.7085 (mtt) cc_final: 0.6817 (mtt) REVERT: f 94 PHE cc_start: 0.6834 (t80) cc_final: 0.6347 (t80) REVERT: f 99 SER cc_start: 0.7742 (t) cc_final: 0.7243 (m) REVERT: g 8 LEU cc_start: 0.8262 (mp) cc_final: 0.8029 (mp) REVERT: g 57 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7410 (ttpp) REVERT: g 89 LEU cc_start: 0.8557 (tp) cc_final: 0.8230 (tp) REVERT: g 125 ASN cc_start: 0.7495 (m-40) cc_final: 0.6696 (t0) REVERT: g 202 LEU cc_start: 0.8728 (tp) cc_final: 0.8409 (tp) REVERT: h 143 MET cc_start: 0.5203 (tmm) cc_final: 0.4767 (ppp) REVERT: i 1 MET cc_start: 0.2114 (tpp) cc_final: 0.1882 (tpp) REVERT: j 29 ILE cc_start: 0.6479 (tp) cc_final: 0.6236 (tp) REVERT: j 56 MET cc_start: 0.0947 (tpp) cc_final: 0.0672 (mmp) REVERT: k 26 MET cc_start: 0.6132 (mtp) cc_final: 0.5853 (mtp) REVERT: k 49 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7474 (ptpp) REVERT: k 74 ILE cc_start: 0.6420 (mm) cc_final: 0.5929 (mm) REVERT: m 62 ARG cc_start: 0.5551 (mtt180) cc_final: 0.5330 (ttm170) REVERT: m 88 MET cc_start: 0.4240 (mtp) cc_final: 0.3903 (mtm) REVERT: n 109 LYS cc_start: 0.6146 (ttpt) cc_final: 0.5939 (ttpt) REVERT: p 32 THR cc_start: 0.7769 (m) cc_final: 0.7562 (m) REVERT: q 67 THR cc_start: 0.7478 (p) cc_final: 0.6965 (p) REVERT: q 93 ILE cc_start: 0.7195 (mp) cc_final: 0.6914 (mp) REVERT: s 21 VAL cc_start: 0.7709 (t) cc_final: 0.7482 (t) REVERT: x 26 MET cc_start: 0.7447 (pmm) cc_final: 0.6544 (pmm) outliers start: 5 outliers final: 1 residues processed: 1689 average time/residue: 1.3813 time to fit residues: 3924.1887 Evaluate side-chains 1452 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1450 time to evaluate : 6.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 578 optimal weight: 9.9990 chunk 741 optimal weight: 20.0000 chunk 574 optimal weight: 6.9990 chunk 855 optimal weight: 40.0000 chunk 567 optimal weight: 8.9990 chunk 1012 optimal weight: 1.9990 chunk 633 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 87 GLN G 138 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN K 82 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 58 ASN b 592 HIS ** b 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 141 HIS ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 39 GLN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS w 8 ASN x 19 HIS x 20 ASN ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 159874 Z= 0.317 Angle : 0.748 16.762 238843 Z= 0.384 Chirality : 0.040 0.290 30483 Planarity : 0.006 0.123 13036 Dihedral : 23.789 177.482 79158 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.17 % Favored : 89.27 % Rotamer: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.10), residues: 6020 helix: -0.82 (0.11), residues: 1777 sheet: -1.43 (0.15), residues: 1006 loop : -2.15 (0.10), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.004 TRP C 212 HIS 0.015 0.002 HIS m 70 PHE 0.067 0.003 PHE Y 26 TYR 0.030 0.003 TYR i 59 ARG 0.017 0.001 ARG U 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1674 time to evaluate : 6.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6924 (ttp80) REVERT: 1 29 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7651 (ttpt) REVERT: 1 45 HIS cc_start: 0.6377 (m90) cc_final: 0.6028 (m-70) REVERT: 2 8 SER cc_start: 0.8920 (t) cc_final: 0.8401 (m) REVERT: 2 9 VAL cc_start: 0.8133 (t) cc_final: 0.7908 (t) REVERT: 2 18 PHE cc_start: 0.8634 (t80) cc_final: 0.8344 (t80) REVERT: 3 32 LEU cc_start: 0.7396 (mt) cc_final: 0.7145 (mt) REVERT: 3 63 TYR cc_start: 0.7330 (m-80) cc_final: 0.7125 (m-10) REVERT: C 115 ILE cc_start: 0.8010 (tt) cc_final: 0.7809 (tt) REVERT: C 128 THR cc_start: 0.8060 (m) cc_final: 0.7459 (m) REVERT: C 129 LEU cc_start: 0.9078 (pt) cc_final: 0.8864 (pt) REVERT: C 184 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6931 (mm-30) REVERT: C 200 MET cc_start: 0.7380 (tpt) cc_final: 0.6863 (tpt) REVERT: C 206 LYS cc_start: 0.8619 (tttm) cc_final: 0.8231 (tttm) REVERT: C 231 HIS cc_start: 0.7395 (m170) cc_final: 0.7175 (m170) REVERT: C 256 THR cc_start: 0.7778 (p) cc_final: 0.7211 (t) REVERT: D 15 PHE cc_start: 0.7101 (m-10) cc_final: 0.6868 (m-10) REVERT: D 43 ASP cc_start: 0.7555 (p0) cc_final: 0.7289 (p0) REVERT: D 149 ASN cc_start: 0.8762 (t0) cc_final: 0.8499 (t0) REVERT: E 1 MET cc_start: 0.4987 (ptm) cc_final: 0.3722 (ttm) REVERT: E 88 ARG cc_start: 0.8151 (mmp80) cc_final: 0.7758 (mmp80) REVERT: E 92 HIS cc_start: 0.5491 (m90) cc_final: 0.5289 (m90) REVERT: E 97 ASN cc_start: 0.7195 (m110) cc_final: 0.6921 (m-40) REVERT: E 100 MET cc_start: 0.8362 (mtm) cc_final: 0.8121 (mtt) REVERT: E 191 ASP cc_start: 0.5520 (t0) cc_final: 0.5217 (t0) REVERT: E 196 VAL cc_start: 0.7947 (p) cc_final: 0.7711 (p) REVERT: E 197 GLU cc_start: 0.8440 (mp0) cc_final: 0.7746 (tt0) REVERT: F 25 MET cc_start: 0.4843 (ttm) cc_final: 0.4175 (ttm) REVERT: G 24 THR cc_start: 0.6111 (m) cc_final: 0.5624 (p) REVERT: G 104 LEU cc_start: 0.8165 (mm) cc_final: 0.7961 (mm) REVERT: H 1 MET cc_start: 0.4468 (ptm) cc_final: 0.3899 (ptp) REVERT: J 44 TYR cc_start: 0.7924 (t80) cc_final: 0.7266 (t80) REVERT: J 45 THR cc_start: 0.8978 (m) cc_final: 0.8397 (m) REVERT: J 54 ILE cc_start: 0.7751 (mt) cc_final: 0.7131 (mt) REVERT: J 77 HIS cc_start: 0.7289 (t-170) cc_final: 0.6759 (t-170) REVERT: J 106 LYS cc_start: 0.7556 (pptt) cc_final: 0.7350 (pptt) REVERT: J 109 LEU cc_start: 0.9084 (mt) cc_final: 0.8483 (mt) REVERT: J 114 LEU cc_start: 0.8682 (tp) cc_final: 0.7721 (tp) REVERT: K 7 MET cc_start: 0.7166 (tpt) cc_final: 0.6038 (mtm) REVERT: L 135 ILE cc_start: 0.8394 (mt) cc_final: 0.8165 (mt) REVERT: M 53 MET cc_start: 0.7691 (mtm) cc_final: 0.7475 (mtm) REVERT: N 1 MET cc_start: 0.7960 (mtm) cc_final: 0.7309 (mtm) REVERT: N 13 ASN cc_start: 0.8013 (p0) cc_final: 0.7768 (p0) REVERT: N 44 LEU cc_start: 0.8406 (tp) cc_final: 0.7431 (tp) REVERT: N 49 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7233 (mt-10) REVERT: N 76 VAL cc_start: 0.7867 (t) cc_final: 0.7641 (t) REVERT: O 31 THR cc_start: 0.4591 (m) cc_final: 0.3955 (m) REVERT: O 39 VAL cc_start: 0.8152 (t) cc_final: 0.7909 (t) REVERT: O 76 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7425 (pttm) REVERT: O 102 ARG cc_start: 0.6879 (mtm180) cc_final: 0.5858 (mtt180) REVERT: P 102 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7423 (tpp-160) REVERT: Q 13 HIS cc_start: 0.8073 (m-70) cc_final: 0.7761 (m170) REVERT: Q 23 TYR cc_start: 0.8147 (m-80) cc_final: 0.7938 (m-80) REVERT: Q 51 GLN cc_start: 0.6115 (mt0) cc_final: 0.5836 (mt0) REVERT: Q 63 ARG cc_start: 0.7635 (mtt180) cc_final: 0.7384 (mtt180) REVERT: Q 97 ILE cc_start: 0.7472 (mt) cc_final: 0.7259 (mt) REVERT: R 43 ASN cc_start: 0.8499 (m-40) cc_final: 0.7978 (m-40) REVERT: S 1 MET cc_start: 0.8215 (tpt) cc_final: 0.8012 (tpt) REVERT: T 2 ILE cc_start: 0.8924 (mm) cc_final: 0.8448 (mt) REVERT: U 3 LYS cc_start: 0.7299 (mttp) cc_final: 0.7005 (mttt) REVERT: V 26 PHE cc_start: 0.7781 (p90) cc_final: 0.7123 (p90) REVERT: V 42 LEU cc_start: 0.6196 (mm) cc_final: 0.5173 (mm) REVERT: V 45 ASP cc_start: 0.7135 (t0) cc_final: 0.6853 (t0) REVERT: V 46 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7330 (mmmt) REVERT: V 92 VAL cc_start: 0.8963 (m) cc_final: 0.8739 (t) REVERT: W 55 LEU cc_start: 0.7773 (mm) cc_final: 0.7458 (mm) REVERT: X 9 LYS cc_start: 0.7012 (mptt) cc_final: 0.6208 (mptt) REVERT: X 57 VAL cc_start: 0.8636 (t) cc_final: 0.8377 (p) REVERT: Y 39 GLN cc_start: 0.6750 (pp30) cc_final: 0.6549 (pm20) REVERT: Y 47 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7716 (ttp-110) REVERT: Z 11 SER cc_start: 0.8213 (t) cc_final: 0.7685 (m) REVERT: Z 37 ARG cc_start: 0.7555 (mmp-170) cc_final: 0.7334 (mmp-170) REVERT: Z 53 MET cc_start: 0.8061 (tmm) cc_final: 0.7483 (ppp) REVERT: b 436 GLU cc_start: 0.8308 (pt0) cc_final: 0.7619 (pm20) REVERT: b 453 SER cc_start: 0.8075 (m) cc_final: 0.7770 (t) REVERT: b 481 GLU cc_start: 0.7660 (mp0) cc_final: 0.7363 (mp0) REVERT: b 485 HIS cc_start: 0.8541 (m90) cc_final: 0.8322 (m-70) REVERT: b 513 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7697 (mm-30) REVERT: b 662 ARG cc_start: 0.6559 (mpp80) cc_final: 0.6287 (mtt-85) REVERT: b 859 MET cc_start: 0.7207 (tmm) cc_final: 0.7005 (tmm) REVERT: d 153 MET cc_start: 0.7029 (mtt) cc_final: 0.6784 (mtt) REVERT: f 63 MET cc_start: 0.6792 (mmm) cc_final: 0.6518 (mmm) REVERT: f 94 PHE cc_start: 0.6699 (t80) cc_final: 0.6329 (t80) REVERT: f 99 SER cc_start: 0.7922 (t) cc_final: 0.7504 (m) REVERT: g 57 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7451 (ttpp) REVERT: g 89 LEU cc_start: 0.8634 (tp) cc_final: 0.8093 (tp) REVERT: g 98 ASP cc_start: 0.7773 (p0) cc_final: 0.7566 (p0) REVERT: g 125 ASN cc_start: 0.7569 (m-40) cc_final: 0.6641 (t0) REVERT: g 202 LEU cc_start: 0.8693 (tp) cc_final: 0.8444 (tp) REVERT: h 140 VAL cc_start: 0.2155 (t) cc_final: 0.1625 (t) REVERT: h 143 MET cc_start: 0.5164 (tmm) cc_final: 0.4841 (ppp) REVERT: i 1 MET cc_start: 0.1841 (tpp) cc_final: 0.1451 (tpp) REVERT: j 29 ILE cc_start: 0.6154 (tp) cc_final: 0.5945 (tp) REVERT: k 49 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7373 (ptpp) REVERT: l 75 GLU cc_start: 0.7016 (pm20) cc_final: 0.6594 (pm20) REVERT: m 11 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7567 (mptt) REVERT: m 88 MET cc_start: 0.4498 (mtp) cc_final: 0.4025 (mtm) REVERT: o 82 ARG cc_start: 0.7354 (ptt90) cc_final: 0.7097 (tmm160) REVERT: p 57 ARG cc_start: 0.8276 (mmm160) cc_final: 0.8031 (tpp-160) REVERT: q 93 ILE cc_start: 0.7206 (mp) cc_final: 0.6934 (mp) REVERT: r 72 TRP cc_start: 0.7543 (m100) cc_final: 0.7194 (m100) REVERT: s 25 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8187 (mtt90) REVERT: x 26 MET cc_start: 0.7153 (pmm) cc_final: 0.6204 (pmm) outliers start: 3 outliers final: 1 residues processed: 1675 average time/residue: 1.3708 time to fit residues: 3869.1652 Evaluate side-chains 1444 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1443 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 604 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 643 optimal weight: 10.0000 chunk 689 optimal weight: 10.0000 chunk 500 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 795 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 82 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 27 ASN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 427 HIS b 532 HIS ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 4 GLN j 80 HIS ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 ASN q 66 GLN ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 159874 Z= 0.240 Angle : 0.682 16.492 238843 Z= 0.352 Chirality : 0.037 0.343 30483 Planarity : 0.006 0.113 13036 Dihedral : 23.760 178.217 79158 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.55 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.32 (0.10), residues: 6020 helix: -0.74 (0.12), residues: 1802 sheet: -1.34 (0.15), residues: 998 loop : -2.11 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 212 HIS 0.013 0.002 HIS m 70 PHE 0.031 0.002 PHE F 76 TYR 0.033 0.002 TYR i 59 ARG 0.028 0.001 ARG P 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1671 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1671 time to evaluate : 6.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 43 THR cc_start: 0.8325 (p) cc_final: 0.7664 (p) REVERT: 1 29 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7702 (ttpt) REVERT: 1 39 ASP cc_start: 0.7240 (p0) cc_final: 0.6934 (p0) REVERT: 1 45 HIS cc_start: 0.6178 (m90) cc_final: 0.5914 (m-70) REVERT: 2 8 SER cc_start: 0.8875 (t) cc_final: 0.8420 (m) REVERT: 2 9 VAL cc_start: 0.8018 (t) cc_final: 0.7706 (t) REVERT: 2 18 PHE cc_start: 0.8614 (t80) cc_final: 0.8243 (t80) REVERT: 2 22 MET cc_start: 0.7087 (tpp) cc_final: 0.6667 (tpp) REVERT: 2 25 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8691 (ptpt) REVERT: 4 3 VAL cc_start: 0.6174 (p) cc_final: 0.5752 (p) REVERT: 4 16 ILE cc_start: 0.8654 (mt) cc_final: 0.8453 (mm) REVERT: 4 25 VAL cc_start: 0.9233 (t) cc_final: 0.9002 (t) REVERT: C 200 MET cc_start: 0.7487 (tpt) cc_final: 0.7037 (tpt) REVERT: C 206 LYS cc_start: 0.8630 (tttm) cc_final: 0.8227 (tttm) REVERT: C 231 HIS cc_start: 0.7286 (m170) cc_final: 0.6968 (m170) REVERT: C 239 PHE cc_start: 0.8355 (t80) cc_final: 0.8134 (t80) REVERT: C 256 THR cc_start: 0.7805 (p) cc_final: 0.7340 (t) REVERT: D 149 ASN cc_start: 0.8580 (t0) cc_final: 0.8338 (t0) REVERT: E 1 MET cc_start: 0.4735 (ptm) cc_final: 0.3556 (ttm) REVERT: E 88 ARG cc_start: 0.8085 (mmp80) cc_final: 0.7414 (mmm-85) REVERT: E 97 ASN cc_start: 0.7168 (m110) cc_final: 0.6747 (m-40) REVERT: E 100 MET cc_start: 0.8249 (mtm) cc_final: 0.7943 (mtt) REVERT: E 197 GLU cc_start: 0.8144 (mp0) cc_final: 0.7827 (tt0) REVERT: F 25 MET cc_start: 0.4817 (ttm) cc_final: 0.4084 (ttm) REVERT: G 24 THR cc_start: 0.5953 (m) cc_final: 0.5585 (p) REVERT: H 1 MET cc_start: 0.4434 (ptm) cc_final: 0.3975 (ptp) REVERT: J 3 THR cc_start: 0.7201 (p) cc_final: 0.7001 (p) REVERT: J 10 THR cc_start: 0.6733 (m) cc_final: 0.6285 (m) REVERT: J 44 TYR cc_start: 0.8161 (t80) cc_final: 0.7485 (t80) REVERT: J 45 THR cc_start: 0.8840 (m) cc_final: 0.8320 (m) REVERT: J 54 ILE cc_start: 0.7604 (mt) cc_final: 0.6973 (mt) REVERT: J 68 LYS cc_start: 0.8470 (mttp) cc_final: 0.8004 (mttp) REVERT: J 70 THR cc_start: 0.8256 (p) cc_final: 0.8003 (p) REVERT: J 77 HIS cc_start: 0.7340 (t-170) cc_final: 0.6792 (t-170) REVERT: J 109 LEU cc_start: 0.9168 (mt) cc_final: 0.8698 (mt) REVERT: J 114 LEU cc_start: 0.8676 (tp) cc_final: 0.7747 (tp) REVERT: K 7 MET cc_start: 0.7094 (tpt) cc_final: 0.6152 (mtm) REVERT: K 23 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7110 (mtpt) REVERT: K 25 LEU cc_start: 0.8465 (mm) cc_final: 0.8262 (mm) REVERT: K 32 TYR cc_start: 0.6899 (m-80) cc_final: 0.6656 (m-10) REVERT: L 2 ARG cc_start: 0.7043 (ttp80) cc_final: 0.6333 (ttt-90) REVERT: L 3 LEU cc_start: 0.8540 (tt) cc_final: 0.8250 (tt) REVERT: L 135 ILE cc_start: 0.8419 (mt) cc_final: 0.8135 (mt) REVERT: M 31 PHE cc_start: 0.7289 (m-80) cc_final: 0.6539 (m-80) REVERT: N 1 MET cc_start: 0.8015 (mtm) cc_final: 0.7360 (mtm) REVERT: N 49 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7219 (mt-10) REVERT: O 7 ARG cc_start: 0.8607 (ptm160) cc_final: 0.8257 (ptm160) REVERT: O 31 THR cc_start: 0.4293 (m) cc_final: 0.3712 (m) REVERT: O 63 LYS cc_start: 0.8634 (pptt) cc_final: 0.8406 (pptt) REVERT: O 76 LYS cc_start: 0.7713 (ptpp) cc_final: 0.7410 (pttm) REVERT: O 102 ARG cc_start: 0.6725 (mtm180) cc_final: 0.5888 (mtt180) REVERT: P 102 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.7393 (tpp-160) REVERT: P 112 ARG cc_start: 0.5589 (tpt170) cc_final: 0.4920 (tpt90) REVERT: Q 13 HIS cc_start: 0.8068 (m-70) cc_final: 0.7740 (m170) REVERT: Q 23 TYR cc_start: 0.8149 (m-80) cc_final: 0.7904 (m-80) REVERT: Q 93 ILE cc_start: 0.8993 (mm) cc_final: 0.8765 (mm) REVERT: R 1 MET cc_start: 0.7829 (tpp) cc_final: 0.7613 (tpt) REVERT: R 43 ASN cc_start: 0.8378 (m-40) cc_final: 0.7913 (m-40) REVERT: T 2 ILE cc_start: 0.8832 (mm) cc_final: 0.8503 (mt) REVERT: T 3 ARG cc_start: 0.6681 (tpt-90) cc_final: 0.6413 (tpt-90) REVERT: U 65 GLN cc_start: 0.7571 (mt0) cc_final: 0.7149 (mt0) REVERT: V 26 PHE cc_start: 0.7726 (p90) cc_final: 0.7125 (p90) REVERT: V 42 LEU cc_start: 0.6298 (mm) cc_final: 0.5575 (mm) REVERT: V 46 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7619 (mmmt) REVERT: V 48 MET cc_start: 0.6898 (mmm) cc_final: 0.6493 (tpp) REVERT: X 9 LYS cc_start: 0.6736 (mptt) cc_final: 0.6524 (mptt) REVERT: Y 47 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7515 (ttp-110) REVERT: b 436 GLU cc_start: 0.8179 (pt0) cc_final: 0.7572 (pm20) REVERT: b 512 ASN cc_start: 0.8817 (p0) cc_final: 0.8530 (p0) REVERT: b 662 ARG cc_start: 0.6438 (mpp80) cc_final: 0.6076 (mtt-85) REVERT: b 782 MET cc_start: 0.7058 (ptm) cc_final: 0.6655 (ttt) REVERT: c 168 ARG cc_start: 0.7260 (tmm160) cc_final: 0.6966 (ttt180) REVERT: d 153 MET cc_start: 0.6972 (mtt) cc_final: 0.6747 (mtt) REVERT: f 94 PHE cc_start: 0.6507 (t80) cc_final: 0.6209 (t80) REVERT: f 99 SER cc_start: 0.8029 (t) cc_final: 0.7638 (m) REVERT: g 89 LEU cc_start: 0.8579 (tp) cc_final: 0.8060 (tp) REVERT: g 98 ASP cc_start: 0.7674 (p0) cc_final: 0.7471 (p0) REVERT: g 125 ASN cc_start: 0.7519 (m-40) cc_final: 0.6630 (t0) REVERT: h 101 ARG cc_start: 0.6507 (ttm170) cc_final: 0.6282 (ttm170) REVERT: h 140 VAL cc_start: 0.2364 (t) cc_final: 0.1674 (t) REVERT: h 143 MET cc_start: 0.5126 (tmm) cc_final: 0.4529 (ppp) REVERT: i 1 MET cc_start: 0.1963 (tpp) cc_final: 0.1461 (tpp) REVERT: j 19 PHE cc_start: 0.5043 (m-80) cc_final: 0.4566 (m-80) REVERT: j 29 ILE cc_start: 0.6196 (tp) cc_final: 0.5945 (tp) REVERT: k 49 LYS cc_start: 0.8251 (ptpp) cc_final: 0.7407 (ptpp) REVERT: k 83 ARG cc_start: 0.8621 (mmt90) cc_final: 0.8352 (mmt-90) REVERT: l 86 LYS cc_start: 0.7587 (pttm) cc_final: 0.7185 (pttm) REVERT: m 11 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7294 (mptt) REVERT: m 62 ARG cc_start: 0.5629 (mtm180) cc_final: 0.5358 (mtm180) REVERT: m 88 MET cc_start: 0.4181 (mtp) cc_final: 0.3849 (mtm) REVERT: p 57 ARG cc_start: 0.8241 (mmm160) cc_final: 0.8039 (tpp-160) REVERT: q 93 ILE cc_start: 0.7328 (mp) cc_final: 0.6988 (mp) REVERT: x 26 MET cc_start: 0.7232 (pmm) cc_final: 0.6181 (pmm) REVERT: x 50 PHE cc_start: 0.5051 (t80) cc_final: 0.4680 (t80) outliers start: 0 outliers final: 0 residues processed: 1671 average time/residue: 1.3720 time to fit residues: 3864.0204 Evaluate side-chains 1449 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1449 time to evaluate : 6.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 1.9990 chunk 969 optimal weight: 5.9990 chunk 884 optimal weight: 9.9990 chunk 943 optimal weight: 9.9990 chunk 567 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 740 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 852 optimal weight: 0.7980 chunk 891 optimal weight: 10.0000 chunk 939 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 62 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN b 592 HIS c 2 GLN ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS u 53 GLN ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 67 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 159874 Z= 0.249 Angle : 0.694 16.411 238843 Z= 0.357 Chirality : 0.037 0.322 30483 Planarity : 0.006 0.113 13036 Dihedral : 23.797 177.163 79158 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 26.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.38 % Favored : 89.10 % Rotamer: Outliers : 0.02 % Allowed : 0.84 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.07 % 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: -2.35 (0.10), residues: 6020 helix: -0.77 (0.12), residues: 1797 sheet: -1.29 (0.15), residues: 1032 loop : -2.16 (0.10), residues: 3191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 212 HIS 0.013 0.002 HIS m 70 PHE 0.025 0.003 PHE i 8 TYR 0.025 0.003 TYR Q 24 ARG 0.021 0.001 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1650 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1649 time to evaluate : 6.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7291 (ttp80) REVERT: 1 29 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7628 (ttpt) REVERT: 1 39 ASP cc_start: 0.7275 (p0) cc_final: 0.6716 (p0) REVERT: 1 43 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7113 (mtp180) REVERT: 2 8 SER cc_start: 0.8766 (t) cc_final: 0.8198 (m) REVERT: 2 9 VAL cc_start: 0.7907 (t) cc_final: 0.7604 (t) REVERT: 2 18 PHE cc_start: 0.8666 (t80) cc_final: 0.8246 (t80) REVERT: 2 22 MET cc_start: 0.7252 (tpp) cc_final: 0.6869 (tpp) REVERT: 3 63 TYR cc_start: 0.7812 (m-80) cc_final: 0.7213 (m-80) REVERT: C 51 ARG cc_start: 0.7402 (ptt-90) cc_final: 0.7166 (ptt180) REVERT: C 128 THR cc_start: 0.7993 (m) cc_final: 0.7754 (m) REVERT: C 200 MET cc_start: 0.7451 (tpt) cc_final: 0.7215 (tpt) REVERT: C 206 LYS cc_start: 0.8554 (tttm) cc_final: 0.8198 (tttm) REVERT: C 256 THR cc_start: 0.7807 (p) cc_final: 0.7346 (t) REVERT: D 149 ASN cc_start: 0.8639 (t0) cc_final: 0.8427 (t0) REVERT: D 173 GLN cc_start: 0.4653 (tm-30) cc_final: 0.4300 (tm-30) REVERT: E 1 MET cc_start: 0.4836 (ptm) cc_final: 0.3364 (ttm) REVERT: E 88 ARG cc_start: 0.8204 (mmp80) cc_final: 0.7921 (mmp80) REVERT: E 97 ASN cc_start: 0.7124 (m110) cc_final: 0.6648 (m-40) REVERT: E 100 MET cc_start: 0.8315 (mtm) cc_final: 0.7998 (mtt) REVERT: F 25 MET cc_start: 0.4976 (ttm) cc_final: 0.4193 (ttm) REVERT: F 33 ILE cc_start: 0.7469 (mm) cc_final: 0.7158 (mm) REVERT: F 51 ASN cc_start: 0.6192 (t0) cc_final: 0.5923 (t0) REVERT: G 24 THR cc_start: 0.6410 (m) cc_final: 0.6073 (p) REVERT: G 104 LEU cc_start: 0.8277 (mm) cc_final: 0.8064 (mm) REVERT: J 10 THR cc_start: 0.6919 (m) cc_final: 0.6516 (m) REVERT: J 44 TYR cc_start: 0.8020 (t80) cc_final: 0.7527 (t80) REVERT: J 45 THR cc_start: 0.8981 (m) cc_final: 0.8366 (m) REVERT: J 54 ILE cc_start: 0.7604 (mt) cc_final: 0.7196 (mt) REVERT: J 68 LYS cc_start: 0.8449 (mttp) cc_final: 0.7774 (mttp) REVERT: J 109 LEU cc_start: 0.9139 (mt) cc_final: 0.8594 (tp) REVERT: J 114 LEU cc_start: 0.8773 (tp) cc_final: 0.7856 (tp) REVERT: K 7 MET cc_start: 0.7184 (tpt) cc_final: 0.6518 (mtm) REVERT: K 25 LEU cc_start: 0.8388 (mm) cc_final: 0.8120 (mm) REVERT: K 32 TYR cc_start: 0.6806 (m-80) cc_final: 0.6173 (m-10) REVERT: K 88 ASN cc_start: 0.7009 (t0) cc_final: 0.5517 (m-40) REVERT: K 115 ILE cc_start: 0.8478 (mp) cc_final: 0.7597 (tp) REVERT: L 73 ILE cc_start: 0.7012 (pt) cc_final: 0.4716 (pt) REVERT: M 31 PHE cc_start: 0.7467 (m-80) cc_final: 0.6987 (m-80) REVERT: M 68 PHE cc_start: 0.7872 (t80) cc_final: 0.7622 (t80) REVERT: N 1 MET cc_start: 0.8014 (mtm) cc_final: 0.7361 (mtm) REVERT: N 28 LEU cc_start: 0.8944 (tt) cc_final: 0.8506 (tp) REVERT: N 49 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7205 (mt-10) REVERT: N 76 VAL cc_start: 0.7924 (t) cc_final: 0.7612 (t) REVERT: N 114 GLU cc_start: 0.5956 (pp20) cc_final: 0.5727 (pp20) REVERT: O 31 THR cc_start: 0.3889 (m) cc_final: 0.3396 (m) REVERT: O 63 LYS cc_start: 0.8574 (pptt) cc_final: 0.8334 (pptt) REVERT: O 76 LYS cc_start: 0.7607 (ptpp) cc_final: 0.7325 (pttm) REVERT: O 102 ARG cc_start: 0.6709 (mtm180) cc_final: 0.6054 (mtt180) REVERT: P 112 ARG cc_start: 0.5303 (tpt170) cc_final: 0.4646 (tpt90) REVERT: Q 13 HIS cc_start: 0.8034 (m-70) cc_final: 0.7786 (m170) REVERT: Q 23 TYR cc_start: 0.8170 (m-80) cc_final: 0.7968 (m-80) REVERT: Q 32 ARG cc_start: 0.8192 (mmp80) cc_final: 0.7989 (mmp80) REVERT: Q 93 ILE cc_start: 0.8974 (mm) cc_final: 0.8730 (mm) REVERT: Q 97 ILE cc_start: 0.7742 (mt) cc_final: 0.7529 (mt) REVERT: R 48 LYS cc_start: 0.6859 (mttt) cc_final: 0.6209 (mttt) REVERT: S 97 LEU cc_start: 0.8515 (tp) cc_final: 0.8145 (tt) REVERT: T 1 MET cc_start: 0.3353 (mtt) cc_final: 0.2843 (mtt) REVERT: T 2 ILE cc_start: 0.8856 (mm) cc_final: 0.8619 (mt) REVERT: U 65 GLN cc_start: 0.7599 (mt0) cc_final: 0.7152 (mt0) REVERT: V 14 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7937 (ptpt) REVERT: V 26 PHE cc_start: 0.7797 (p90) cc_final: 0.7132 (p90) REVERT: V 42 LEU cc_start: 0.6234 (mm) cc_final: 0.5852 (mm) REVERT: V 46 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7310 (mmmt) REVERT: V 48 MET cc_start: 0.6987 (mmm) cc_final: 0.6097 (tpp) REVERT: W 55 LEU cc_start: 0.7780 (mm) cc_final: 0.7544 (mm) REVERT: Y 29 ARG cc_start: 0.8707 (pmt170) cc_final: 0.8450 (pmt170) REVERT: Z 53 MET cc_start: 0.7573 (ppp) cc_final: 0.7352 (ppp) REVERT: b 436 GLU cc_start: 0.8190 (pt0) cc_final: 0.7611 (pm20) REVERT: b 782 MET cc_start: 0.7084 (ptm) cc_final: 0.6677 (ttt) REVERT: b 839 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6615 (tp30) REVERT: c 168 ARG cc_start: 0.7246 (tmm160) cc_final: 0.6889 (ttt180) REVERT: f 70 MET cc_start: 0.4119 (mmp) cc_final: 0.3305 (mmm) REVERT: f 94 PHE cc_start: 0.6561 (t80) cc_final: 0.6262 (t80) REVERT: f 99 SER cc_start: 0.8006 (t) cc_final: 0.7569 (m) REVERT: g 89 LEU cc_start: 0.8634 (tp) cc_final: 0.8185 (tp) REVERT: g 125 ASN cc_start: 0.7612 (m-40) cc_final: 0.6736 (t0) REVERT: h 39 GLU cc_start: 0.7171 (tt0) cc_final: 0.6649 (tp30) REVERT: h 101 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6217 (ttm170) REVERT: h 140 VAL cc_start: 0.2833 (t) cc_final: 0.2143 (t) REVERT: h 143 MET cc_start: 0.4753 (tmm) cc_final: 0.4263 (ppp) REVERT: i 1 MET cc_start: 0.1416 (tpp) cc_final: 0.0662 (tpp) REVERT: j 19 PHE cc_start: 0.5197 (m-80) cc_final: 0.4546 (m-80) REVERT: j 29 ILE cc_start: 0.6258 (tp) cc_final: 0.5910 (tp) REVERT: k 49 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7431 (ptpp) REVERT: l 25 SER cc_start: 0.7184 (t) cc_final: 0.6465 (t) REVERT: l 86 LYS cc_start: 0.7764 (pttm) cc_final: 0.7355 (pttm) REVERT: l 96 ILE cc_start: 0.8474 (tp) cc_final: 0.7808 (tt) REVERT: m 11 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7376 (mptt) REVERT: n 16 ILE cc_start: 0.7844 (pt) cc_final: 0.7093 (mp) REVERT: p 32 THR cc_start: 0.7408 (m) cc_final: 0.6819 (m) REVERT: p 62 ARG cc_start: 0.7231 (ptm160) cc_final: 0.6676 (ttt180) REVERT: q 17 ASP cc_start: 0.6016 (p0) cc_final: 0.5520 (p0) REVERT: q 93 ILE cc_start: 0.7289 (mp) cc_final: 0.6966 (mp) REVERT: r 17 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6545 (mm-30) REVERT: s 14 ARG cc_start: 0.7354 (mtp180) cc_final: 0.7152 (mtp180) REVERT: u 53 GLN cc_start: 0.7586 (mt0) cc_final: 0.7233 (mp10) REVERT: x 26 MET cc_start: 0.7174 (pmm) cc_final: 0.6491 (pmm) outliers start: 1 outliers final: 0 residues processed: 1649 average time/residue: 1.4832 time to fit residues: 4183.7358 Evaluate side-chains 1440 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1440 time to evaluate : 6.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 20.0000 chunk 997 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 473 optimal weight: 0.9980 chunk 693 optimal weight: 20.0000 chunk 1046 optimal weight: 8.9990 chunk 962 optimal weight: 2.9990 chunk 832 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 643 optimal weight: 10.0000 chunk 510 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 49 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS K 82 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 43 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 27 ASN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 159874 Z= 0.249 Angle : 0.691 16.296 238843 Z= 0.356 Chirality : 0.037 0.326 30483 Planarity : 0.006 0.130 13036 Dihedral : 23.829 177.666 79158 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.25 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.36 (0.10), residues: 6020 helix: -0.81 (0.12), residues: 1802 sheet: -1.19 (0.15), residues: 1035 loop : -2.18 (0.10), residues: 3183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP t 33 HIS 0.011 0.002 HIS t 51 PHE 0.032 0.002 PHE D 82 TYR 0.031 0.002 TYR d 212 ARG 0.019 0.001 ARG p 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12040 Ramachandran restraints generated. 6020 Oldfield, 0 Emsley, 6020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1631 time to evaluate : 6.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 29 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7564 (ttpt) REVERT: 1 39 ASP cc_start: 0.7238 (p0) cc_final: 0.6848 (p0) REVERT: 1 43 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7641 (mtp180) REVERT: 1 45 HIS cc_start: 0.6134 (m-70) cc_final: 0.5842 (m-70) REVERT: 2 8 SER cc_start: 0.8779 (t) cc_final: 0.8276 (m) REVERT: 2 9 VAL cc_start: 0.7874 (t) cc_final: 0.7585 (t) REVERT: 2 18 PHE cc_start: 0.8711 (t80) cc_final: 0.8289 (t80) REVERT: 2 22 MET cc_start: 0.7303 (tpp) cc_final: 0.6888 (tpp) REVERT: 3 63 TYR cc_start: 0.7741 (m-80) cc_final: 0.7217 (m-80) REVERT: 4 24 ARG cc_start: 0.7334 (mmm-85) cc_final: 0.6996 (mmm-85) REVERT: C 71 ASP cc_start: 0.8603 (m-30) cc_final: 0.8324 (m-30) REVERT: C 128 THR cc_start: 0.7956 (m) cc_final: 0.7669 (m) REVERT: C 129 LEU cc_start: 0.9171 (pt) cc_final: 0.8857 (pt) REVERT: C 173 LEU cc_start: 0.7638 (mp) cc_final: 0.7431 (mp) REVERT: C 200 MET cc_start: 0.7566 (tpt) cc_final: 0.7217 (tpt) REVERT: C 206 LYS cc_start: 0.8463 (tttm) cc_final: 0.8102 (tttm) REVERT: C 256 THR cc_start: 0.7805 (p) cc_final: 0.7344 (t) REVERT: D 149 ASN cc_start: 0.8588 (t0) cc_final: 0.8378 (t0) REVERT: E 1 MET cc_start: 0.4533 (ptm) cc_final: 0.3235 (ttm) REVERT: E 88 ARG cc_start: 0.8184 (mmp80) cc_final: 0.7431 (mmm-85) REVERT: E 97 ASN cc_start: 0.7099 (m110) cc_final: 0.6407 (m-40) REVERT: E 100 MET cc_start: 0.8269 (mtm) cc_final: 0.7931 (mtt) REVERT: E 197 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8090 (mm-30) REVERT: F 25 MET cc_start: 0.5092 (ttm) cc_final: 0.4373 (ttm) REVERT: F 104 THR cc_start: 0.6847 (p) cc_final: 0.6380 (t) REVERT: F 127 TYR cc_start: 0.3955 (t80) cc_final: 0.3699 (t80) REVERT: G 24 THR cc_start: 0.6956 (m) cc_final: 0.6403 (p) REVERT: G 41 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6271 (mm-30) REVERT: G 104 LEU cc_start: 0.8235 (mm) cc_final: 0.7962 (mm) REVERT: J 10 THR cc_start: 0.7141 (m) cc_final: 0.6584 (m) REVERT: J 44 TYR cc_start: 0.7994 (t80) cc_final: 0.7059 (t80) REVERT: J 45 THR cc_start: 0.8951 (m) cc_final: 0.8262 (m) REVERT: J 54 ILE cc_start: 0.7796 (mt) cc_final: 0.7312 (mt) REVERT: J 65 THR cc_start: 0.7940 (p) cc_final: 0.7707 (p) REVERT: J 77 HIS cc_start: 0.7175 (t-170) cc_final: 0.6808 (t-170) REVERT: J 114 LEU cc_start: 0.8680 (tp) cc_final: 0.7937 (tp) REVERT: K 7 MET cc_start: 0.7039 (tpt) cc_final: 0.6547 (mtm) REVERT: K 32 TYR cc_start: 0.6959 (m-80) cc_final: 0.6659 (m-10) REVERT: K 82 ASN cc_start: 0.8200 (m-40) cc_final: 0.7956 (m-40) REVERT: K 88 ASN cc_start: 0.7084 (t0) cc_final: 0.5823 (m-40) REVERT: K 115 ILE cc_start: 0.8515 (mp) cc_final: 0.7633 (tp) REVERT: L 73 ILE cc_start: 0.6848 (pt) cc_final: 0.4618 (pt) REVERT: M 31 PHE cc_start: 0.7545 (m-80) cc_final: 0.7160 (m-80) REVERT: M 68 PHE cc_start: 0.8156 (t80) cc_final: 0.7882 (t80) REVERT: N 1 MET cc_start: 0.8014 (mtm) cc_final: 0.7433 (mtm) REVERT: N 24 MET cc_start: 0.7067 (ttp) cc_final: 0.6764 (ttp) REVERT: N 28 LEU cc_start: 0.8901 (tt) cc_final: 0.8570 (tp) REVERT: N 44 LEU cc_start: 0.8420 (tp) cc_final: 0.8217 (tp) REVERT: N 49 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7223 (mt-10) REVERT: N 76 VAL cc_start: 0.7671 (t) cc_final: 0.7418 (t) REVERT: O 31 THR cc_start: 0.4345 (m) cc_final: 0.3716 (m) REVERT: O 76 LYS cc_start: 0.7596 (ptpp) cc_final: 0.7331 (pttm) REVERT: O 102 ARG cc_start: 0.6804 (mtm180) cc_final: 0.6000 (mtt180) REVERT: P 38 ARG cc_start: 0.7012 (ttm170) cc_final: 0.5953 (ttm170) REVERT: P 83 ILE cc_start: 0.8609 (mp) cc_final: 0.8399 (mp) REVERT: P 102 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7341 (tpp80) REVERT: P 110 LYS cc_start: 0.7944 (tptp) cc_final: 0.7711 (ptpt) REVERT: P 112 ARG cc_start: 0.5533 (tpt170) cc_final: 0.4713 (tpt90) REVERT: Q 13 HIS cc_start: 0.8002 (m-70) cc_final: 0.7756 (m170) REVERT: Q 23 TYR cc_start: 0.8212 (m-80) cc_final: 0.7980 (m-80) REVERT: Q 47 ARG cc_start: 0.6402 (ttp-170) cc_final: 0.6165 (ttp80) REVERT: Q 93 ILE cc_start: 0.8985 (mm) cc_final: 0.8781 (mm) REVERT: R 48 LYS cc_start: 0.7065 (mttt) cc_final: 0.6614 (mttt) REVERT: S 61 ASN cc_start: 0.8229 (m-40) cc_final: 0.7616 (m-40) REVERT: T 1 MET cc_start: 0.3747 (mtt) cc_final: 0.3466 (mtt) REVERT: U 65 GLN cc_start: 0.7601 (mt0) cc_final: 0.7245 (mt0) REVERT: U 72 PHE cc_start: 0.6922 (t80) cc_final: 0.6560 (t80) REVERT: V 26 PHE cc_start: 0.7835 (p90) cc_final: 0.7514 (p90) REVERT: V 42 LEU cc_start: 0.6461 (mm) cc_final: 0.6035 (mm) REVERT: V 46 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7618 (mmmt) REVERT: V 48 MET cc_start: 0.7061 (mmm) cc_final: 0.6231 (tpp) REVERT: W 79 GLU cc_start: 0.8489 (mp0) cc_final: 0.8181 (mp0) REVERT: Y 29 ARG cc_start: 0.8733 (pmt170) cc_final: 0.8490 (pmt170) REVERT: Y 56 LEU cc_start: 0.8747 (mm) cc_final: 0.8460 (mm) REVERT: b 436 GLU cc_start: 0.8196 (pt0) cc_final: 0.7613 (pm20) REVERT: b 481 GLU cc_start: 0.7647 (mp0) cc_final: 0.7207 (mp0) REVERT: b 592 HIS cc_start: 0.8092 (t70) cc_final: 0.7783 (p90) REVERT: b 748 VAL cc_start: 0.8029 (p) cc_final: 0.7806 (t) REVERT: b 782 MET cc_start: 0.7104 (ptm) cc_final: 0.6725 (ttt) REVERT: c 168 ARG cc_start: 0.7247 (tmm160) cc_final: 0.6839 (ttt180) REVERT: c 202 PHE cc_start: 0.7251 (t80) cc_final: 0.7009 (t80) REVERT: d 67 LEU cc_start: 0.8281 (tt) cc_final: 0.7792 (mm) REVERT: d 115 ASP cc_start: 0.6862 (t0) cc_final: 0.6435 (t0) REVERT: d 116 LEU cc_start: 0.6688 (tt) cc_final: 0.6340 (tt) REVERT: d 140 LEU cc_start: 0.6509 (mp) cc_final: 0.6176 (mp) REVERT: f 70 MET cc_start: 0.5108 (mmp) cc_final: 0.3907 (mmm) REVERT: f 94 PHE cc_start: 0.6462 (t80) cc_final: 0.6102 (t80) REVERT: f 99 SER cc_start: 0.8185 (t) cc_final: 0.7788 (m) REVERT: g 89 LEU cc_start: 0.8839 (tp) cc_final: 0.8331 (tp) REVERT: g 125 ASN cc_start: 0.7589 (m-40) cc_final: 0.6802 (t0) REVERT: g 196 GLU cc_start: 0.6108 (mp0) cc_final: 0.5807 (mp0) REVERT: h 39 GLU cc_start: 0.7201 (tt0) cc_final: 0.6750 (tp30) REVERT: h 101 ARG cc_start: 0.6857 (ttm170) cc_final: 0.6564 (ttm170) REVERT: h 143 MET cc_start: 0.4059 (tmm) cc_final: 0.3769 (ppp) REVERT: i 1 MET cc_start: 0.2159 (tpp) cc_final: 0.1230 (tpp) REVERT: j 19 PHE cc_start: 0.5185 (m-80) cc_final: 0.4485 (m-80) REVERT: k 49 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7423 (ptpp) REVERT: k 84 ILE cc_start: 0.8355 (mp) cc_final: 0.7701 (mp) REVERT: l 86 LYS cc_start: 0.7664 (pttm) cc_final: 0.7393 (pttm) REVERT: l 96 ILE cc_start: 0.8461 (tp) cc_final: 0.7773 (tt) REVERT: m 11 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7360 (mptt) REVERT: m 71 LEU cc_start: 0.7990 (tt) cc_final: 0.7656 (tt) REVERT: n 16 ILE cc_start: 0.8057 (pt) cc_final: 0.7396 (mp) REVERT: q 17 ASP cc_start: 0.6018 (p0) cc_final: 0.5510 (p0) REVERT: q 93 ILE cc_start: 0.7324 (mp) cc_final: 0.7032 (mp) REVERT: u 53 GLN cc_start: 0.7815 (pm20) cc_final: 0.7443 (pm20) REVERT: w 46 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7611 (mmp80) REVERT: x 26 MET cc_start: 0.7607 (pmm) cc_final: 0.6848 (pmm) outliers start: 0 outliers final: 0 residues processed: 1631 average time/residue: 1.3854 time to fit residues: 3825.1932 Evaluate side-chains 1430 residues out of total 4995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1430 time to evaluate : 5.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 20.0000 chunk 887 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 768 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 834 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 856 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN g 88 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 HIS x 47 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101354 restraints weight = 483897.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104385 restraints weight = 207146.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.106152 restraints weight = 112195.245| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 159874 Z= 0.278 Angle : 0.721 16.236 238843 Z= 0.370 Chirality : 0.038 0.344 30483 Planarity : 0.006 0.219 13036 Dihedral : 23.922 178.951 79158 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 29.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.93 % Favored : 88.57 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.07 % 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: -2.45 (0.10), residues: 6020 helix: -0.88 (0.12), residues: 1792 sheet: -1.24 (0.15), residues: 1050 loop : -2.24 (0.10), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP t 33 HIS 0.014 0.002 HIS m 70 PHE 0.031 0.003 PHE i 8 TYR 0.032 0.003 TYR J 125 ARG 0.029 0.001 ARG P 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50780.16 seconds wall clock time: 882 minutes 28.64 seconds (52948.64 seconds total)