Starting phenix.real_space_refine on Sun Mar 24 14:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/03_2024/3jcj_6559_neut_trim_updated.pdb" } resolution = 3.7 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= 0.091 sd= 0.658 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4597 5.49 5 Mg 195 5.21 5 S 166 5.16 5 C 74493 2.51 5 N 27411 2.21 5 O 41484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "F ARG 2": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "P ARG 2": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 93": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 76": "NH1" <-> "NH2" Residue "W ARG 2": "NH1" <-> "NH2" Residue "W ARG 10": "NH1" <-> "NH2" Residue "W ARG 17": "NH1" <-> "NH2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 44": "NH1" <-> "NH2" Residue "Z ARG 9": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "a ARG 43": "NH1" <-> "NH2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 12": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 19": "NH1" <-> "NH2" Residue "b ARG 21": "NH1" <-> "NH2" Residue "b ARG 33": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 29": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 24": "NH1" <-> "NH2" Residue "f ARG 390": "NH1" <-> "NH2" Residue "f ARG 412": "NH1" <-> "NH2" Residue "f ARG 455": "NH1" <-> "NH2" Residue "f ARG 561": "NH1" <-> "NH2" Residue "f ARG 587": "NH1" <-> "NH2" Residue "f ARG 605": "NH1" <-> "NH2" Residue "f ARG 607": "NH1" <-> "NH2" Residue "f ARG 610": "NH1" <-> "NH2" Residue "f ARG 662": "NH1" <-> "NH2" Residue "f ARG 668": "NH1" <-> "NH2" Residue "f ARG 766": "NH1" <-> "NH2" Residue "f ARG 829": "NH1" <-> "NH2" Residue "f ARG 846": "NH1" <-> "NH2" Residue "f GLU 884": "OE1" <-> "OE2" Residue "f ARG 887": "NH1" <-> "NH2" Residue "h ARG 130": "NH1" <-> "NH2" Residue "o PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 123": "NH1" <-> "NH2" Residue "t ARG 55": "NH1" <-> "NH2" Residue "y 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: 148347 Number of models: 1 Model: "" Number of chains: 82 Chain: "0" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "1" 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: "2" 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: "3" 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: "4" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 61274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2854, 61274 Classifications: {'RNA': 2854} Modifications used: {'rna2p_pur': 266, 'rna2p_pyr': 144, 'rna3p_pur': 1382, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 410, 'rna3p': 2443} Chain breaks: 3 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "H" 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: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" 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: "L" 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: "M" 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: "N" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "S" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "U" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "V" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "W" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "a" 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: "b" 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: "c" 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: "d" 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: "e" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 884 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "f" 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: "g" 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: "h" 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: "j" 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: "k" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "l" 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: "m" 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: "n" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 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: "p" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "q" Number of atoms: 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: "r" 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: "s" 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: "t" 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: "u" 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: "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: 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: "x" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "y" Number of atoms: 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: "z" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Unusual residues: {' MG': 137} Classifications: {'undetermined': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Unusual residues: {' MG': 54} Classifications: {'undetermined': 54} Link IDs: {None: 53} 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 Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 599 Classifications: {'water': 599} Link IDs: {None: 598} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90668 SG CYS d 11 119.179 143.801 174.334 1.00 32.46 S ATOM 90693 SG CYS d 14 116.489 145.992 173.524 1.00 36.60 S Time building chain proxies: 57.98, per 1000 atoms: 0.39 Number of scatterers: 148347 At special positions: 0 Unit cell: (266.5, 282.9, 232.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 166 16.00 P 4597 15.00 Mg 195 11.99 O 41484 8.00 N 27411 7.00 C 74493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS f 815 " - pdb=" SG CYS f 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.71 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 102 " pdb="ZN ZN d 102 " - pdb=" SG CYS d 14 " pdb="ZN ZN d 102 " - pdb=" SG CYS d 11 " 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11462 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 62 sheets defined 36.4% alpha, 14.9% beta 1063 base pairs and 2653 stacking pairs defined. Time for finding SS restraints: 76.89 Creating SS restraints... Processing helix chain '1' and resid 24 through 33 removed outlier: 5.216A pdb=" N ASN 1 30 " --> pdb=" O ALA 1 26 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR 1 31 " --> pdb=" O THR 1 27 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR 1 33 " --> pdb=" O LYS 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 45 removed outlier: 3.762A pdb=" N THR 1 44 " --> pdb=" O PRO 1 40 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 65 Processing helix chain '2' and resid 17 through 22 removed outlier: 3.768A pdb=" N SER 2 21 " --> pdb=" O ARG 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 33 removed outlier: 4.186A pdb=" N ARG 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 52 removed outlier: 3.708A pdb=" N ALA 2 47 " --> pdb=" O GLU 2 43 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS 2 48 " --> pdb=" O ARG 2 44 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL 2 52 " --> pdb=" O LYS 2 48 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 39 removed outlier: 3.670A pdb=" N ILE 3 11 " --> pdb=" O LYS 3 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER 3 22 " --> pdb=" O LYS 3 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE 3 30 " --> pdb=" O MET 3 26 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE 3 31 " --> pdb=" O MET 3 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 3 34 " --> pdb=" O PHE 3 30 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA 3 36 " --> pdb=" O LYS 3 32 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA 3 37 " --> pdb=" O LYS 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 64 removed outlier: 3.812A pdb=" N ALA 3 46 " --> pdb=" O ASP 3 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN 3 47 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) Proline residue: 3 55 - end of helix removed outlier: 3.596A pdb=" N ASP 3 58 " --> pdb=" O GLN 3 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA 3 61 " --> pdb=" O VAL 3 57 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 86 removed outlier: 5.421A pdb=" N ALA 3 71 " --> pdb=" O HIS 3 67 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS 3 75 " --> pdb=" O ALA 3 71 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA 3 80 " --> pdb=" O ALA 3 76 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN 3 81 " --> pdb=" O ASN 3 77 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN 3 83 " --> pdb=" O THR 3 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 3 84 " --> pdb=" O ALA 3 80 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU 3 85 " --> pdb=" O GLN 3 81 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA 3 86 " --> pdb=" O ILE 3 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 4.451A pdb=" N VAL B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.725A pdb=" N ILE B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix No H-bonds generated for 'chain 'B' and resid 130 through 135' Processing helix chain 'B' and resid 206 through 214 removed outlier: 4.683A pdb=" N ALA B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 214' Processing helix chain 'B' and resid 220 through 225 removed outlier: 4.272A pdb=" N MET B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 225' Processing helix chain 'B' and resid 259 through 267 removed outlier: 6.024A pdb=" N ASP B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS B 264 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 267' Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.827A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.455A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.624A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 4.357A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 105' Processing helix chain 'C' and resid 121 through 126 removed outlier: 6.799A pdb=" N TRP C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'D' and resid 24 through 40 removed outlier: 4.031A pdb=" N VAL D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLY D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 6.190A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.773A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.592A pdb=" N ALA D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.981A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.697A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 10 removed outlier: 3.788A pdb=" N ASP E 9 " --> pdb=" O ASP E 5 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.135A pdb=" N LEU E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.815A pdb=" N ASP E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 92 through 111 removed outlier: 4.082A pdb=" N TRP E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 98 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 5.613A pdb=" N ARG E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.880A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 removed outlier: 3.816A pdb=" N ILE E 136 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 137 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Proline residue: E 138 - end of helix No H-bonds generated for 'chain 'E' and resid 133 through 138' Processing helix chain 'F' and resid 60 through 80 removed outlier: 4.954A pdb=" N ALA F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA F 67 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.503A pdb=" N GLN F 142 " --> pdb=" O GLN F 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 removed outlier: 3.551A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 50 removed outlier: 6.942A pdb=" N ILE G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 50' Processing helix chain 'H' and resid 33 through 49 removed outlier: 3.968A pdb=" N PHE H 37 " --> pdb=" O ASN H 33 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS H 38 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS H 39 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN H 42 " --> pdb=" O CYS H 38 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP H 46 " --> pdb=" O ASN H 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 removed outlier: 3.976A pdb=" N LEU H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 removed outlier: 5.144A pdb=" N LEU H 105 " --> pdb=" O SER H 101 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN H 110 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 113' Processing helix chain 'H' and resid 120 through 136 removed outlier: 3.607A pdb=" N MET H 124 " --> pdb=" O ASP H 120 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR H 125 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG H 126 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE H 128 " --> pdb=" O MET H 124 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 24 removed outlier: 4.848A pdb=" N LYS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 19 through 24' Processing helix chain 'I' and resid 25 through 38 removed outlier: 6.152A pdb=" N ALA I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 removed outlier: 4.236A pdb=" N ARG I 96 " --> pdb=" O MET I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 4.605A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 123 removed outlier: 3.610A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 119 removed outlier: 3.625A pdb=" N ILE J 116 " --> pdb=" O PHE J 112 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU J 118 " --> pdb=" O LYS J 114 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA J 119 " --> pdb=" O ILE J 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 119' Processing helix chain 'J' and resid 104 through 109 removed outlier: 4.473A pdb=" N SER J 109 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 42 removed outlier: 4.258A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 37 through 42' Processing helix chain 'K' and resid 56 through 61 removed outlier: 3.787A pdb=" N LEU K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 75 removed outlier: 4.025A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR K 74 " --> pdb=" O LYS K 70 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 69 through 75' Processing helix chain 'K' and resid 81 through 86 removed outlier: 6.910A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 81 through 86' Processing helix chain 'K' and resid 94 through 99 removed outlier: 4.370A pdb=" N ALA K 98 " --> pdb=" O THR K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 139 removed outlier: 4.359A pdb=" N ALA K 133 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 57 removed outlier: 3.630A pdb=" N ILE L 46 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG L 55 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA L 56 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 125 removed outlier: 3.904A pdb=" N GLU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 122 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Proline residue: L 125 - end of helix Processing helix chain 'M' and resid 13 through 32 removed outlier: 3.551A pdb=" N ALA M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG M 22 " --> pdb=" O GLN M 18 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 58 removed outlier: 3.583A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 3.626A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 removed outlier: 3.651A pdb=" N ARG M 63 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 82 removed outlier: 3.678A pdb=" N VAL M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE M 80 " --> pdb=" O VAL M 76 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU M 82 " --> pdb=" O LYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 89 removed outlier: 4.482A pdb=" N SER M 89 " --> pdb=" O PRO M 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 22 removed outlier: 4.257A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 86 removed outlier: 3.526A pdb=" N ALA N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 114 removed outlier: 3.695A pdb=" N ALA N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA N 107 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP N 108 " --> pdb=" O GLN N 104 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA N 110 " --> pdb=" O LEU N 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 13 removed outlier: 4.793A pdb=" N LYS O 5 " --> pdb=" O SER O 1 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN O 6 " --> pdb=" O ASN O 2 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU O 7 " --> pdb=" O ILE O 3 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU O 8 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU O 10 " --> pdb=" O GLN O 6 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN O 11 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS O 13 " --> pdb=" O GLN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 removed outlier: 4.030A pdb=" N ARG O 102 " --> pdb=" O TYR O 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 21 removed outlier: 6.397A pdb=" N ALA P 9 " --> pdb=" O ARG P 5 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA P 11 " --> pdb=" O VAL P 7 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 16 " --> pdb=" O ARG P 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS P 21 " --> pdb=" O LEU P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 30 removed outlier: 4.250A pdb=" N ARG P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 59 removed outlier: 3.569A pdb=" N ARG P 49 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG P 50 " --> pdb=" O TYR P 46 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS P 53 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 72 Processing helix chain 'P' and resid 74 through 85 Processing helix chain 'P' and resid 91 through 101 removed outlier: 4.263A pdb=" N ALA P 95 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP P 96 " --> pdb=" O LYS P 92 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE P 97 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL P 99 " --> pdb=" O ALA P 95 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 117 removed outlier: 3.534A pdb=" N THR P 106 " --> pdb=" O LYS P 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA P 107 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU P 108 " --> pdb=" O ALA P 104 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA P 114 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 25 removed outlier: 6.917A pdb=" N VAL R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 removed outlier: 3.847A pdb=" N ASP R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 61 removed outlier: 3.904A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 9 removed outlier: 3.814A pdb=" N LEU S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS S 9 " --> pdb=" O GLU S 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 4 through 9' Processing helix chain 'S' and resid 18 through 25 removed outlier: 3.551A pdb=" N ALA S 23 " --> pdb=" O LYS S 19 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET S 24 " --> pdb=" O ALA S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 51 removed outlier: 3.792A pdb=" N ILE S 43 " --> pdb=" O THR S 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 46 " --> pdb=" O GLU S 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE S 51 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 70 removed outlier: 4.032A pdb=" N VAL T 69 " --> pdb=" O GLN T 65 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA T 70 " --> pdb=" O VAL T 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 65 through 70' Processing helix chain 'U' and resid 13 through 24 removed outlier: 3.788A pdb=" N ARG U 19 " --> pdb=" O GLY U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 53 removed outlier: 4.498A pdb=" N ASN U 49 " --> pdb=" O ASP U 45 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET U 50 " --> pdb=" O LYS U 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 59 removed outlier: 3.761A pdb=" N SER U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 removed outlier: 3.671A pdb=" N MET W 55 " --> pdb=" O SER W 51 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG W 56 " --> pdb=" O ALA W 52 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL W 57 " --> pdb=" O LYS W 53 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP W 59 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS W 60 " --> pdb=" O ARG W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 71 removed outlier: 3.574A pdb=" N VAL W 66 " --> pdb=" O GLY W 62 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU W 70 " --> pdb=" O VAL W 66 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 7 removed outlier: 3.992A pdb=" N LEU X 6 " --> pdb=" O LYS X 2 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG X 7 " --> pdb=" O ALA X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 35 removed outlier: 4.500A pdb=" N LEU X 14 " --> pdb=" O SER X 10 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN X 15 " --> pdb=" O VAL X 11 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR X 16 " --> pdb=" O GLU X 12 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN X 25 " --> pdb=" O LEU X 21 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE X 26 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN X 27 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA X 33 " --> pdb=" O ARG X 29 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 62 removed outlier: 3.957A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL X 46 " --> pdb=" O LEU X 42 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG X 47 " --> pdb=" O LEU X 43 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG X 48 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP X 49 " --> pdb=" O GLN X 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA X 51 " --> pdb=" O ARG X 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU X 57 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU X 59 " --> pdb=" O THR X 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS X 60 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY X 62 " --> pdb=" O ASN X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.626A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY Y 45 " --> pdb=" O PRO Y 41 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET Y 46 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 20 removed outlier: 4.921A pdb=" N HIS Z 18 " --> pdb=" O MET Z 14 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP Z 19 " --> pdb=" O ARG Z 15 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 30 Proline residue: a 30 - end of helix Processing helix chain 'b' and resid 8 through 16 removed outlier: 3.583A pdb=" N ARG b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 24 removed outlier: 4.502A pdb=" N THR b 24 " --> pdb=" O ALA b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 38 removed outlier: 3.569A pdb=" N GLN b 29 " --> pdb=" O LYS b 25 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL b 30 " --> pdb=" O ASN b 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU b 31 " --> pdb=" O GLY b 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 14 removed outlier: 3.718A pdb=" N LYS c 11 " --> pdb=" O ARG c 7 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG c 12 " --> pdb=" O GLY c 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE c 13 " --> pdb=" O ALA c 9 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS c 14 " --> pdb=" O ALA c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 36 removed outlier: 4.590A pdb=" N LYS c 35 " --> pdb=" O ILE c 31 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA c 36 " --> pdb=" O LEU c 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 31 through 36' Processing helix chain 'c' and resid 37 through 45 removed outlier: 3.852A pdb=" N HIS c 42 " --> pdb=" O LYS c 38 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Proline residue: c 45 - end of helix Processing helix chain 'c' and resid 51 through 62 removed outlier: 4.646A pdb=" N GLY c 55 " --> pdb=" O LYS c 51 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU c 56 " --> pdb=" O GLY c 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL c 57 " --> pdb=" O ASP c 53 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA c 59 " --> pdb=" O GLY c 55 " (cutoff:3.500A) Proline residue: c 62 - end of helix Processing helix chain 'e' and resid 6 through 21 removed outlier: 4.667A pdb=" N ALA e 10 " --> pdb=" O GLN e 6 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE e 11 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU e 14 " --> pdb=" O ALA e 10 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU e 17 " --> pdb=" O ALA e 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL e 18 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA e 19 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 46 removed outlier: 3.595A pdb=" N THR e 39 " --> pdb=" O VAL e 35 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU e 40 " --> pdb=" O ASP e 36 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 62 through 68 removed outlier: 3.530A pdb=" N GLY e 66 " --> pdb=" O ARG e 62 " (cutoff:3.500A) Proline residue: e 68 - end of helix Processing helix chain 'e' and resid 94 through 104 removed outlier: 4.062A pdb=" N GLU e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE e 99 " --> pdb=" O LEU e 95 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ALA e 104 " --> pdb=" O ALA e 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 413 removed outlier: 3.901A pdb=" N LEU f 408 " --> pdb=" O LYS f 404 " (cutoff:3.500A) Processing helix chain 'f' and resid 451 through 463 removed outlier: 3.873A pdb=" N ARG f 455 " --> pdb=" O PHE f 451 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA f 456 " --> pdb=" O THR f 452 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN f 460 " --> pdb=" O ALA f 456 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR f 462 " --> pdb=" O GLY f 458 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP f 463 " --> pdb=" O ALA f 459 " (cutoff:3.500A) Processing helix chain 'f' and resid 476 through 490 removed outlier: 3.503A pdb=" N GLN f 484 " --> pdb=" O ILE f 480 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS f 485 " --> pdb=" O GLU f 481 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA f 489 " --> pdb=" O HIS f 485 " (cutoff:3.500A) Processing helix chain 'f' and resid 506 through 518 removed outlier: 4.087A pdb=" N VAL f 510 " --> pdb=" O ASP f 506 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN f 516 " --> pdb=" O ASN f 512 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR f 517 " --> pdb=" O GLU f 513 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY f 518 " --> pdb=" O LEU f 514 " (cutoff:3.500A) Processing helix chain 'f' and resid 540 through 556 removed outlier: 5.817A pdb=" N LEU f 544 " --> pdb=" O GLY f 540 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU f 555 " --> pdb=" O GLN f 551 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU f 556 " --> pdb=" O ALA f 552 " (cutoff:3.500A) Processing helix chain 'f' and resid 648 through 676 removed outlier: 4.341A pdb=" N GLU f 652 " --> pdb=" O LYS f 648 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL f 653 " --> pdb=" O LYS f 649 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS f 673 " --> pdb=" O GLN f 669 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN f 676 " --> pdb=" O SER f 672 " (cutoff:3.500A) Processing helix chain 'f' and resid 697 through 713 removed outlier: 4.063A pdb=" N VAL f 701 " --> pdb=" O VAL f 697 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU f 702 " --> pdb=" O GLN f 698 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA f 703 " --> pdb=" O GLY f 699 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER f 705 " --> pdb=" O VAL f 701 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP f 706 " --> pdb=" O GLU f 702 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER f 707 " --> pdb=" O ALA f 703 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU f 711 " --> pdb=" O SER f 707 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER f 712 " --> pdb=" O LEU f 708 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR f 713 " --> pdb=" O LEU f 709 " (cutoff:3.500A) Processing helix chain 'f' and resid 729 through 740 removed outlier: 3.911A pdb=" N SER f 739 " --> pdb=" O LEU f 735 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN f 740 " --> pdb=" O ALA f 736 " (cutoff:3.500A) Processing helix chain 'f' and resid 751 through 762 removed outlier: 3.927A pdb=" N LYS f 756 " --> pdb=" O ALA f 752 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL f 757 " --> pdb=" O SER f 753 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER f 762 " --> pdb=" O ILE f 758 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 786 removed outlier: 3.734A pdb=" N LEU f 774 " --> pdb=" O VAL f 770 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU f 777 " --> pdb=" O ASN f 773 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS f 779 " --> pdb=" O ILE f 775 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU f 786 " --> pdb=" O MET f 782 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 12 removed outlier: 3.503A pdb=" N LEU h 11 " --> pdb=" O ASN h 7 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY h 12 " --> pdb=" O GLY h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 47 removed outlier: 3.566A pdb=" N SER h 34 " --> pdb=" O ASP h 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE h 36 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG h 39 " --> pdb=" O ASP h 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS h 44 " --> pdb=" O GLN h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 77 removed outlier: 3.810A pdb=" N VAL h 75 " --> pdb=" O ARG h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 95 removed outlier: 3.526A pdb=" N GLU h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS h 85 " --> pdb=" O GLU h 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU h 86 " --> pdb=" O ASP h 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 126 removed outlier: 3.544A pdb=" N VAL h 115 " --> pdb=" O ASP h 111 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU h 123 " --> pdb=" O ILE h 119 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU h 124 " --> pdb=" O THR h 120 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 144 removed outlier: 3.921A pdb=" N ALA h 136 " --> pdb=" O ALA h 132 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN h 139 " --> pdb=" O ARG h 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N MET h 141 " --> pdb=" O VAL h 137 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG h 142 " --> pdb=" O GLN h 138 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU h 143 " --> pdb=" O ASN h 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY h 144 " --> pdb=" O ALA h 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 23 through 28 removed outlier: 3.935A pdb=" N LYS j 27 " --> pdb=" O ASN j 23 " (cutoff:3.500A) Proline residue: j 28 - end of helix No H-bonds generated for 'chain 'j' and resid 23 through 28' Processing helix chain 'j' and resid 42 through 63 Proline residue: j 47 - end of helix removed outlier: 4.005A pdb=" N ASN j 50 " --> pdb=" O VAL j 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU j 51 " --> pdb=" O PRO j 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN j 57 " --> pdb=" O LEU j 53 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS j 58 " --> pdb=" O ALA j 54 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE j 59 " --> pdb=" O GLU j 55 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA j 60 " --> pdb=" O LEU j 56 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER j 61 " --> pdb=" O ASN j 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG j 62 " --> pdb=" O LYS j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 103 removed outlier: 3.638A pdb=" N TRP j 103 " --> pdb=" O MET j 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 120 removed outlier: 4.638A pdb=" N GLN j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER j 109 " --> pdb=" O THR j 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE j 110 " --> pdb=" O VAL j 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS j 111 " --> pdb=" O ARG j 107 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN j 119 " --> pdb=" O ASP j 115 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER j 120 " --> pdb=" O LEU j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 129 through 148 removed outlier: 4.509A pdb=" N ARG j 136 " --> pdb=" O GLU j 132 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU j 139 " --> pdb=" O MET j 135 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU j 140 " --> pdb=" O ARG j 136 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU j 141 " --> pdb=" O THR j 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS j 142 " --> pdb=" O ARG j 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN j 145 " --> pdb=" O GLU j 141 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER j 146 " --> pdb=" O LYS j 142 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 154 removed outlier: 5.667A pdb=" N MET j 153 " --> pdb=" O GLY j 149 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY j 154 " --> pdb=" O ILE j 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 149 through 154' Processing helix chain 'j' and resid 164 through 169 Processing helix chain 'j' and resid 170 through 179 removed outlier: 3.545A pdb=" N GLU j 174 " --> pdb=" O ILE j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 205 through 221 removed outlier: 3.744A pdb=" N VAL j 209 " --> pdb=" O ALA j 205 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR j 210 " --> pdb=" O ILE j 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA j 215 " --> pdb=" O LEU j 211 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR j 219 " --> pdb=" O ALA j 215 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL j 220 " --> pdb=" O VAL j 216 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG j 221 " --> pdb=" O ALA j 217 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 81 removed outlier: 4.051A pdb=" N LYS j 80 " --> pdb=" O GLU j 77 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP j 81 " --> pdb=" O ALA j 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 69 removed outlier: 3.731A pdb=" N ARG k 67 " --> pdb=" O MET k 63 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG k 68 " --> pdb=" O GLU k 64 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN k 69 " --> pdb=" O LYS k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 118 removed outlier: 7.157A pdb=" N ALA k 112 " --> pdb=" O GLY k 108 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL k 113 " --> pdb=" O ALA k 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU k 114 " --> pdb=" O MET k 110 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA k 117 " --> pdb=" O VAL k 113 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY k 118 " --> pdb=" O LEU k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 131 through 153 removed outlier: 3.824A pdb=" N VAL k 136 " --> pdb=" O PRO k 132 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG k 137 " --> pdb=" O ILE k 133 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA k 138 " --> pdb=" O ASN k 134 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR k 139 " --> pdb=" O VAL k 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE k 140 " --> pdb=" O VAL k 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET k 146 " --> pdb=" O GLY k 142 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASN k 147 " --> pdb=" O LEU k 143 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER k 148 " --> pdb=" O GLU k 144 " (cutoff:3.500A) Proline residue: k 149 - end of helix removed outlier: 4.259A pdb=" N ALA k 153 " --> pdb=" O PRO k 149 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 15 removed outlier: 3.860A pdb=" N LEU l 10 " --> pdb=" O PRO l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 65 removed outlier: 3.997A pdb=" N GLN l 53 " --> pdb=" O ASP l 49 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE l 63 " --> pdb=" O LYS l 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 67 through 82 removed outlier: 3.553A pdb=" N TYR l 74 " --> pdb=" O GLN l 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG l 80 " --> pdb=" O LYS l 76 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS l 82 " --> pdb=" O ALA l 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 96 removed outlier: 3.699A pdb=" N LEU l 90 " --> pdb=" O GLY l 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 105 Processing helix chain 'l' and resid 109 through 120 removed outlier: 3.622A pdb=" N HIS l 119 " --> pdb=" O GLN l 115 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS l 120 " --> pdb=" O LEU l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 151 through 165 removed outlier: 3.693A pdb=" N ALA l 157 " --> pdb=" O ARG l 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU l 160 " --> pdb=" O ALA l 156 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU l 162 " --> pdb=" O LEU l 158 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN l 163 " --> pdb=" O GLU l 159 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG l 164 " --> pdb=" O LEU l 160 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU l 165 " --> pdb=" O ALA l 161 " (cutoff:3.500A) Processing helix chain 'l' and resid 186 through 191 removed outlier: 3.645A pdb=" N LEU l 190 " --> pdb=" O GLU l 186 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER l 191 " --> pdb=" O ARG l 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 186 through 191' Processing helix chain 'l' and resid 195 through 205 removed outlier: 4.040A pdb=" N ILE l 199 " --> pdb=" O ASN l 195 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU l 201 " --> pdb=" O HIS l 197 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU l 202 " --> pdb=" O LEU l 198 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR l 203 " --> pdb=" O ILE l 199 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER l 204 " --> pdb=" O VAL l 200 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS l 205 " --> pdb=" O GLU l 201 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 30 removed outlier: 3.565A pdb=" N ALA m 23 " --> pdb=" O SER m 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS m 24 " --> pdb=" O GLU m 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN m 27 " --> pdb=" O ALA m 23 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 54 removed outlier: 3.616A pdb=" N SER m 40 " --> pdb=" O SER m 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE m 41 " --> pdb=" O THR m 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR m 48 " --> pdb=" O SER m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 57 through 69 removed outlier: 4.415A pdb=" N PHE m 61 " --> pdb=" O GLU m 57 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU m 62 " --> pdb=" O LEU m 58 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL m 68 " --> pdb=" O ALA m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 91 through 111 removed outlier: 3.773A pdb=" N ASN m 96 " --> pdb=" O PRO m 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA m 97 " --> pdb=" O VAL m 93 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL m 104 " --> pdb=" O MET m 100 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS m 109 " --> pdb=" O GLU m 105 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLY m 111 " --> pdb=" O ALA m 107 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 127 removed outlier: 4.506A pdb=" N ALA m 127 " --> pdb=" O LEU m 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 131 through 148 removed outlier: 3.750A pdb=" N LYS m 135 " --> pdb=" O GLY m 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU m 138 " --> pdb=" O VAL m 134 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP m 139 " --> pdb=" O LYS m 135 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL m 140 " --> pdb=" O LYS m 136 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS m 141 " --> pdb=" O ARG m 137 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG m 142 " --> pdb=" O GLU m 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET m 143 " --> pdb=" O ASP m 139 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU m 145 " --> pdb=" O HIS m 141 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA m 146 " --> pdb=" O ARG m 142 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 31 removed outlier: 4.064A pdb=" N VAL n 18 " --> pdb=" O GLN n 14 " (cutoff:3.500A) Proline residue: n 19 - end of helix removed outlier: 3.667A pdb=" N GLU n 23 " --> pdb=" O PRO n 19 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 82 removed outlier: 3.779A pdb=" N ASP n 72 " --> pdb=" O GLN n 68 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU n 73 " --> pdb=" O GLU n 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR n 76 " --> pdb=" O ASP n 72 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP n 82 " --> pdb=" O PHE n 78 " (cutoff:3.500A) Processing helix chain 'o' and resid 33 through 38 removed outlier: 4.304A pdb=" N PHE o 38 " --> pdb=" O LEU o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 45 through 53 Proline residue: o 50 - end of helix removed outlier: 5.150A pdb=" N LEU o 53 " --> pdb=" O GLN o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 70 through 86 removed outlier: 3.769A pdb=" N GLN o 74 " --> pdb=" O GLY o 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG o 84 " --> pdb=" O HIS o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 90 through 101 removed outlier: 4.409A pdb=" N ARG o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER o 95 " --> pdb=" O GLU o 91 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU o 96 " --> pdb=" O SER o 92 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS o 99 " --> pdb=" O SER o 95 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA o 100 " --> pdb=" O GLU o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 20 removed outlier: 3.554A pdb=" N MET p 9 " --> pdb=" O PRO p 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG p 14 " --> pdb=" O LEU p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 29 through 43 removed outlier: 3.516A pdb=" N VAL p 33 " --> pdb=" O SER p 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA p 34 " --> pdb=" O LYS p 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA p 36 " --> pdb=" O LYS p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 111 through 119 removed outlier: 3.726A pdb=" N ARG p 116 " --> pdb=" O ASP p 112 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN p 117 " --> pdb=" O ARG p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 45 through 50 removed outlier: 3.878A pdb=" N GLY q 50 " --> pdb=" O ALA q 46 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 58 removed outlier: 4.191A pdb=" N SER q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR q 58 " --> pdb=" O SER q 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 53 through 58' Processing helix chain 'q' and resid 59 through 74 removed outlier: 3.701A pdb=" N GLN q 63 " --> pdb=" O PRO q 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG q 68 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA q 72 " --> pdb=" O ARG q 68 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL q 73 " --> pdb=" O CYS q 69 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 92 through 103 removed outlier: 4.129A pdb=" N ILE q 96 " --> pdb=" O ARG q 92 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG q 97 " --> pdb=" O GLU q 93 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA q 98 " --> pdb=" O SER q 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU q 99 " --> pdb=" O THR q 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA q 101 " --> pdb=" O ARG q 97 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY q 103 " --> pdb=" O LEU q 99 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 33 removed outlier: 6.234A pdb=" N GLN r 20 " --> pdb=" O ARG r 16 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL r 26 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU r 27 " --> pdb=" O ALA r 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG r 31 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) Processing helix chain 'r' and resid 80 through 88 removed outlier: 4.104A pdb=" N ASP r 85 " --> pdb=" O GLU r 81 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA r 86 " --> pdb=" O LYS r 82 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU r 87 " --> pdb=" O THR r 83 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET r 88 " --> pdb=" O VAL r 84 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 21 removed outlier: 3.765A pdb=" N THR s 19 " --> pdb=" O VAL s 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER s 20 " --> pdb=" O ILE s 16 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 25 through 37 removed outlier: 3.712A pdb=" N LYS s 30 " --> pdb=" O LYS s 26 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU s 33 " --> pdb=" O SER s 29 " (cutoff:3.500A) Processing helix chain 's' and resid 48 through 63 removed outlier: 3.911A pdb=" N ASP s 53 " --> pdb=" O GLU s 49 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR s 54 " --> pdb=" O GLY s 50 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU s 55 " --> pdb=" O GLN s 51 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE s 62 " --> pdb=" O GLU s 58 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL s 63 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 83 removed outlier: 4.318A pdb=" N GLY s 83 " --> pdb=" O LEU s 79 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 93 removed outlier: 3.725A pdb=" N ARG s 91 " --> pdb=" O GLY s 87 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY s 93 " --> pdb=" O ARG s 89 " (cutoff:3.500A) Processing helix chain 's' and resid 105 through 110 removed outlier: 4.265A pdb=" N GLY s 110 " --> pdb=" O ALA s 105 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 105 through 110' Processing helix chain 't' and resid 2 through 10 removed outlier: 3.516A pdb=" N LEU t 6 " --> pdb=" O THR t 2 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG t 8 " --> pdb=" O ASN t 4 " (cutoff:3.500A) Proline residue: t 10 - end of helix Processing helix chain 't' and resid 112 through 117 removed outlier: 4.989A pdb=" N TYR t 116 " --> pdb=" O ALA t 112 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY t 117 " --> pdb=" O ARG t 113 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 112 through 117' Processing helix chain 'u' and resid 3 through 15 removed outlier: 3.642A pdb=" N ILE u 10 " --> pdb=" O ALA u 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU u 13 " --> pdb=" O LYS u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 43 removed outlier: 3.661A pdb=" N LEU u 31 " --> pdb=" O GLN u 27 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY u 40 " --> pdb=" O ASN u 36 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS u 41 " --> pdb=" O HIS u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 48 through 73 removed outlier: 3.736A pdb=" N ARG u 52 " --> pdb=" O ASP u 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG u 53 " --> pdb=" O HIS u 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY u 54 " --> pdb=" O HIS u 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET u 58 " --> pdb=" O GLY u 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS u 64 " --> pdb=" O SER u 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG u 71 " --> pdb=" O ASP u 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS u 72 " --> pdb=" O TYR u 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 74 through 85 removed outlier: 3.605A pdb=" N GLN u 79 " --> pdb=" O ALA u 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 19 removed outlier: 4.037A pdb=" N ALA w 16 " --> pdb=" O ARG w 12 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP w 17 " --> pdb=" O VAL w 13 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS w 18 " --> pdb=" O ALA w 14 " (cutoff:3.500A) Processing helix chain 'w' and resid 24 through 29 removed outlier: 4.716A pdb=" N ALA w 28 " --> pdb=" O ALA w 24 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE w 29 " --> pdb=" O GLU w 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 24 through 29' Processing helix chain 'w' and resid 43 through 49 removed outlier: 3.559A pdb=" N LYS w 47 " --> pdb=" O ASN w 43 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU w 48 " --> pdb=" O ALA w 44 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN w 49 " --> pdb=" O VAL w 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 43 through 49' Processing helix chain 'w' and resid 80 through 91 removed outlier: 3.539A pdb=" N ARG w 90 " --> pdb=" O GLU w 86 " (cutoff:3.500A) Processing helix chain 'y' and resid 53 through 64 removed outlier: 3.651A pdb=" N ILE y 57 " --> pdb=" O ASP y 53 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS y 59 " --> pdb=" O ASP y 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP y 60 " --> pdb=" O ARG y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 79 Processing helix chain 'z' and resid 11 through 24 removed outlier: 3.521A pdb=" N LYS z 17 " --> pdb=" O HIS z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 69 through 75 removed outlier: 4.443A pdb=" N PHE z 73 " --> pdb=" O LYS z 69 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA z 74 " --> pdb=" O LEU z 70 " (cutoff:3.500A) Proline residue: z 75 - end of helix No H-bonds generated for 'chain 'z' and resid 69 through 75' Processing helix chain 'z' and resid 63 through 68 removed outlier: 4.043A pdb=" N VAL z 66 " --> pdb=" O ASP z 63 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY z 67 " --> pdb=" O GLU z 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 79 through 82 removed outlier: 4.724A pdb=" N ARG B 79 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.975A pdb=" N THR B 172 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 3 through 7 removed outlier: 6.240A pdb=" N LYS C 204 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 10 through 16 removed outlier: 5.066A pdb=" N VAL C 26 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 24 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 14 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 22 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 16 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.608A pdb=" N ARG C 33 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.856A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET D 188 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 147 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 187 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE D 149 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D 148 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 64 through 67 removed outlier: 3.842A pdb=" N GLY E 85 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS E 86 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 32 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET E 129 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE E 155 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR E 127 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 14 through 18 removed outlier: 3.772A pdb=" N ASP F 15 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS F 26 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN F 21 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN F 37 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 84 through 88 removed outlier: 4.634A pdb=" N LYS F 84 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU F 132 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR F 128 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA F 135 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N GLY F 119 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 93 through 98 removed outlier: 4.295A pdb=" N ARG F 94 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 105 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN F 103 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 7 through 12 removed outlier: 4.278A pdb=" N VAL H 8 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE H 58 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU H 10 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 56 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'J' and resid 5 through 10 removed outlier: 4.992A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS J 21 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG J 17 " --> pdb=" O VAL J 10 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'J' and resid 38 through 42 Processing sheet with id= 14, first strand: chain 'L' and resid 103 through 106 removed outlier: 3.853A pdb=" N GLY L 32 " --> pdb=" O VAL L 131 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL L 131 " --> pdb=" O GLY L 32 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'M' and resid 33 through 36 removed outlier: 5.772A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.959A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS N 34 " --> pdb=" O THR N 31 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL N 28 " --> pdb=" O ASP N 93 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'O' and resid 25 through 32 Processing sheet with id= 18, first strand: chain 'O' and resid 56 through 63 removed outlier: 7.941A pdb=" N SER O 56 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL O 69 " --> pdb=" O LYS O 62 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Q' and resid 1 through 4 removed outlier: 4.250A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 19 through 24 removed outlier: 4.080A pdb=" N VAL Q 20 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS Q 24 " --> pdb=" O TRP Q 92 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TRP Q 92 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS Q 89 " --> pdb=" O VAL Q 72 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL Q 72 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 32 through 36 Processing sheet with id= 22, first strand: chain 'R' and resid 2 through 8 removed outlier: 4.694A pdb=" N THR R 3 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL R 107 " --> pdb=" O THR R 3 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'R' and resid 80 through 86 removed outlier: 4.305A pdb=" N THR R 100 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG R 84 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE R 96 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP R 94 " --> pdb=" O MET R 86 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'S' and resid 28 through 34 removed outlier: 4.650A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU S 87 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE S 30 " --> pdb=" O VAL S 85 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU S 32 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL S 34 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'T' and resid 25 through 28 removed outlier: 4.385A pdb=" N LYS T 32 " --> pdb=" O LEU T 28 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'T' and resid 40 through 43 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'U' and resid 61 through 64 removed outlier: 3.963A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE U 29 " --> pdb=" O ILE U 89 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP U 76 " --> pdb=" O ASP U 90 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'V' and resid 42 through 45 removed outlier: 6.379A pdb=" N PHE V 44 " --> pdb=" O LYS V 77 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE V 78 " --> pdb=" O GLU V 69 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU V 69 " --> pdb=" O PHE V 78 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER V 80 " --> pdb=" O LYS V 67 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'W' and resid 11 through 15 Processing sheet with id= 30, first strand: chain 'Y' and resid 34 through 38 removed outlier: 3.711A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR Y 7 " --> pdb=" O LYS Y 55 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'a' and resid 7 through 11 removed outlier: 3.643A pdb=" N TYR a 20 " --> pdb=" O LEU a 10 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'a' and resid 32 through 38 removed outlier: 6.878A pdb=" N LEU a 33 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU a 50 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU a 35 " --> pdb=" O TYR a 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS a 37 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 14 through 18 removed outlier: 6.577A pdb=" N ILE d 26 " --> pdb=" O LYS d 15 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL d 17 " --> pdb=" O ARG d 24 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG d 24 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'f' and resid 428 through 432 removed outlier: 4.034A pdb=" N GLY f 429 " --> pdb=" O ASP f 444 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP f 444 " --> pdb=" O GLY f 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR f 441 " --> pdb=" O PRO f 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL f 394 " --> pdb=" O THR f 441 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR f 445 " --> pdb=" O ILE f 396 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY f 398 " --> pdb=" O THR f 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA f 496 " --> pdb=" O LEU f 467 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 571 through 575 removed outlier: 3.556A pdb=" N GLU f 571 " --> pdb=" O THR f 583 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR f 583 " --> pdb=" O ILE f 570 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER f 566 " --> pdb=" O ARG f 587 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA f 565 " --> pdb=" O VAL f 643 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP f 639 " --> pdb=" O VAL f 569 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE f 596 " --> pdb=" O VAL f 644 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'f' and resid 608 through 611 removed outlier: 4.030A pdb=" N ALA f 608 " --> pdb=" O LEU f 629 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU f 629 " --> pdb=" O ALA f 608 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 717 through 721 removed outlier: 3.646A pdb=" N LYS f 719 " --> pdb=" O VAL f 689 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU f 693 " --> pdb=" O ILE f 721 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE f 742 " --> pdb=" O ASN f 690 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE f 746 " --> pdb=" O LYS f 694 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP f 764 " --> pdb=" O ALA f 741 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY f 745 " --> pdb=" O ARG f 766 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'f' and resid 798 through 801 Processing sheet with id= 39, first strand: chain 'f' and resid 820 through 824 removed outlier: 6.925A pdb=" N GLY f 820 " --> pdb=" O ASN f 857 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ASN f 853 " --> pdb=" O ARG f 824 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 827 through 830 Processing sheet with id= 41, first strand: chain 'f' and resid 812 through 816 Processing sheet with id= 42, first strand: chain 'h' and resid 53 through 58 removed outlier: 4.609A pdb=" N ARG h 53 " --> pdb=" O HIS h 68 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU h 57 " --> pdb=" O ARG h 64 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE h 63 " --> pdb=" O PRO h 97 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL h 65 " --> pdb=" O GLN h 99 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN h 101 " --> pdb=" O VAL h 65 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE h 67 " --> pdb=" O ASN h 101 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'h' and resid 146 through 154 removed outlier: 3.548A pdb=" N GLY h 196 " --> pdb=" O SER h 153 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR h 190 " --> pdb=" O GLY h 193 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE h 195 " --> pdb=" O ALA h 188 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL h 199 " --> pdb=" O ASN h 184 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN h 184 " --> pdb=" O VAL h 199 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP h 180 " --> pdb=" O LYS h 203 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 29 through 32 removed outlier: 7.243A pdb=" N PHE j 29 " --> pdb=" O ASN j 41 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE j 39 " --> pdb=" O PHE j 31 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'j' and resid 66 through 70 removed outlier: 4.894A pdb=" N LEU j 67 " --> pdb=" O ALA j 159 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL j 162 " --> pdb=" O PHE j 183 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'k' and resid 10 through 15 removed outlier: 4.331A pdb=" N GLN k 11 " --> pdb=" O GLY k 39 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY k 39 " --> pdb=" O GLN k 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS k 13 " --> pdb=" O VAL k 37 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU k 35 " --> pdb=" O ILE k 15 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'k' and resid 70 through 73 removed outlier: 5.823A pdb=" N VAL k 73 " --> pdb=" O GLY k 43 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY k 43 " --> pdb=" O VAL k 73 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'k' and resid 92 through 97 removed outlier: 4.270A pdb=" N PHE k 94 " --> pdb=" O LYS k 125 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS k 125 " --> pdb=" O PHE k 94 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN k 96 " --> pdb=" O LEU k 123 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'k' and resid 31 through 39 removed outlier: 4.246A pdb=" N ALA k 34 " --> pdb=" O GLY k 50 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY k 50 " --> pdb=" O ALA k 34 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'l' and resid 140 through 143 removed outlier: 4.048A pdb=" N ASP l 140 " --> pdb=" O PHE l 181 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE l 181 " --> pdb=" O ASP l 140 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 72 through 78 removed outlier: 6.497A pdb=" N TYR m 84 " --> pdb=" O ARG m 77 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'n' and resid 39 through 43 removed outlier: 3.731A pdb=" N VAL n 60 " --> pdb=" O PHE n 8 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE n 6 " --> pdb=" O MET n 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR n 4 " --> pdb=" O VAL n 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS n 3 " --> pdb=" O THR n 92 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR n 92 " --> pdb=" O HIS n 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU n 5 " --> pdb=" O MET n 90 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG n 86 " --> pdb=" O MET n 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 5 through 10 removed outlier: 4.070A pdb=" N TYR o 5 " --> pdb=" O ILE o 20 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY o 9 " --> pdb=" O ALA o 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR o 65 " --> pdb=" O ARG o 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR o 63 " --> pdb=" O PHE o 19 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 22 through 27 removed outlier: 5.895A pdb=" N ALA p 22 " --> pdb=" O LEU p 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU p 57 " --> pdb=" O GLU p 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP p 47 " --> pdb=" O THR p 61 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'p' and resid 122 through 125 removed outlier: 6.659A pdb=" N VAL p 102 " --> pdb=" O ILE p 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE p 100 " --> pdb=" O VAL p 128 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS p 126 " --> pdb=" O VAL p 102 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 41 through 44 removed outlier: 4.424A pdb=" N ASN q 108 " --> pdb=" O LEU q 81 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY q 87 " --> pdb=" O VAL q 112 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'r' and resid 44 through 52 removed outlier: 3.554A pdb=" N ARG r 72 " --> pdb=" O LEU r 10 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE r 8 " --> pdb=" O VAL r 74 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE r 76 " --> pdb=" O ILE r 6 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE r 6 " --> pdb=" O ILE r 76 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 35 through 40 removed outlier: 4.393A pdb=" N ARG t 35 " --> pdb=" O ARG t 53 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG t 49 " --> pdb=" O THR t 39 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS t 50 " --> pdb=" O ILE t 66 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE t 60 " --> pdb=" O LEU t 56 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'x' and resid 19 through 27 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'x' and resid 59 through 62 removed outlier: 6.928A pdb=" N GLU x 59 " --> pdb=" O VAL x 75 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'y' and resid 4 through 8 removed outlier: 3.729A pdb=" N VAL y 19 " --> pdb=" O GLY y 37 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY y 37 " --> pdb=" O VAL y 19 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'z' and resid 47 through 51 removed outlier: 3.680A pdb=" N ILE z 48 " --> pdb=" O VAL z 59 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2520 hydrogen bonds 3968 hydrogen bond angles 0 basepair planarities 1063 basepair parallelities 2653 stacking parallelities Total time for adding SS restraints: 366.86 Time building geometry restraints manager: 65.15 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: 20654 1.33 - 1.45: 67381 1.45 - 1.57: 62270 1.57 - 1.69: 9190 1.69 - 1.81: 300 Bond restraints: 159795 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 f 901 " pdb=" C2' GNP f 901 " ideal model delta sigma weight residual 1.273 1.521 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C3' GNP f 901 " pdb=" C4' GNP f 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 1.388 -0.233 2.00e-02 2.50e+03 1.35e+02 ... (remaining 159790 not shown) Histogram of bond angle deviations from ideal: 96.53 - 105.17: 21040 105.17 - 113.81: 99543 113.81 - 122.46: 81307 122.46 - 131.10: 35287 131.10 - 139.74: 1326 Bond angle restraints: 238503 Sorted by residual: angle pdb=" O3' C v 23 " pdb=" C3' C v 23 " pdb=" C2' C v 23 " ideal model delta sigma weight residual 113.70 97.80 15.90 1.50e+00 4.44e-01 1.12e+02 angle pdb=" C4' G g 115 " pdb=" C3' G g 115 " pdb=" O3' G g 115 " ideal model delta sigma weight residual 109.40 121.55 -12.15 1.50e+00 4.44e-01 6.56e+01 angle pdb=" C4' A A1020 " pdb=" C3' A A1020 " pdb=" O3' A A1020 " ideal model delta sigma weight residual 109.40 121.54 -12.14 1.50e+00 4.44e-01 6.55e+01 angle pdb=" C4' A A 503 " pdb=" C3' A A 503 " pdb=" O3' A A 503 " ideal model delta sigma weight residual 109.40 121.40 -12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" C4' A A 404 " pdb=" C3' A A 404 " pdb=" O3' A A 404 " ideal model delta sigma weight residual 109.40 121.34 -11.94 1.50e+00 4.44e-01 6.34e+01 ... (remaining 238498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 92616 35.96 - 71.91: 8424 71.91 - 107.87: 1186 107.87 - 143.83: 11 143.83 - 179.79: 25 Dihedral angle restraints: 102262 sinusoidal: 84482 harmonic: 17780 Sorted by residual: dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 45.83 154.17 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U A2076 " pdb=" C1' U A2076 " pdb=" N1 U A2076 " pdb=" C2 U A2076 " ideal model delta sinusoidal sigma weight residual 200.00 49.77 150.23 1 1.50e+01 4.44e-03 7.97e+01 dihedral pdb=" O4' C g 754 " pdb=" C1' C g 754 " pdb=" N1 C g 754 " pdb=" C2 C g 754 " ideal model delta sinusoidal sigma weight residual 200.00 51.47 148.53 1 1.50e+01 4.44e-03 7.91e+01 ... (remaining 102259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 25108 0.142 - 0.284: 5252 0.284 - 0.425: 41 0.425 - 0.567: 7 0.567 - 0.709: 4 Chirality restraints: 30412 Sorted by residual: 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 1.26e+01 chirality pdb=" C3' A g1201 " pdb=" C4' A g1201 " pdb=" O3' A g1201 " pdb=" C2' A g1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" C3' G g 115 " pdb=" C4' G g 115 " pdb=" O3' G g 115 " pdb=" C2' G g 115 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.57 2.00e-01 2.50e+01 8.12e+00 ... (remaining 30409 not shown) Planarity restraints: 13162 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 " -0.431 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 " 0.192 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 " 0.359 2.00e-02 2.50e+03 pdb=" N1 5MU v 54 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP f 901 " -0.359 2.00e-02 2.50e+03 3.87e-01 3.38e+03 pdb=" C2' GNP f 901 " 0.439 2.00e-02 2.50e+03 pdb=" C3' GNP f 901 " 0.442 2.00e-02 2.50e+03 pdb=" C4' GNP f 901 " -0.358 2.00e-02 2.50e+03 pdb=" C5' GNP f 901 " 0.385 2.00e-02 2.50e+03 pdb=" N9 GNP f 901 " 0.398 2.00e-02 2.50e+03 pdb=" O2' GNP f 901 " -0.192 2.00e-02 2.50e+03 pdb=" O3' GNP f 901 " -0.183 2.00e-02 2.50e+03 pdb=" O4' GNP f 901 " -0.572 2.00e-02 2.50e+03 ... (remaining 13159 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 165 2.06 - 2.77: 17585 2.77 - 3.48: 191418 3.48 - 4.19: 458190 4.19 - 4.90: 627915 Nonbonded interactions: 1295273 Sorted by model distance: nonbonded pdb=" O SER f 534 " pdb=" O6 GNP f 901 " model vdw 1.344 3.040 nonbonded pdb="MG MG g1608 " pdb=" O HOH g1740 " model vdw 1.480 2.170 nonbonded pdb=" O2* PSU v 55 " pdb=" O5' C v 56 " model vdw 1.485 3.040 nonbonded pdb=" OP2 C g 352 " pdb="MG MG g1609 " model vdw 1.606 2.170 nonbonded pdb="MG MG A3125 " pdb=" O HOH A3732 " model vdw 1.624 2.170 ... (remaining 1295268 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=0.89 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 15.050 Check model and map are aligned: 1.630 Set scattering table: 0.970 Process input model: 689.210 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 715.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 159795 Z= 0.464 Angle : 1.046 15.905 238503 Z= 0.695 Chirality : 0.097 0.709 30412 Planarity : 0.007 0.394 13162 Dihedral : 21.227 179.785 90797 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 1.77 % Allowed : 9.23 % Favored : 89.00 % Rotamer: Outliers : 0.39 % Allowed : 2.42 % Favored : 97.19 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -3.55 (0.09), residues: 6144 helix: -2.57 (0.09), residues: 1517 sheet: -2.44 (0.15), residues: 866 loop : -2.31 (0.09), residues: 3761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 21 HIS 0.007 0.001 HIS q 117 PHE 0.019 0.002 PHE j 49 TYR 0.018 0.002 TYR P 23 ARG 0.009 0.001 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2069 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 2049 time to evaluate : 6.510 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: B 43 ASN cc_start: 0.7776 (t0) cc_final: 0.7275 (t0) REVERT: C 186 LEU cc_start: 0.7877 (mp) cc_final: 0.7609 (mp) REVERT: D 162 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6955 (ttp-170) REVERT: D 176 ASP cc_start: 0.7158 (p0) cc_final: 0.6879 (p0) REVERT: F 71 LEU cc_start: 0.7396 (mt) cc_final: 0.7194 (mt) REVERT: I 21 THR cc_start: 0.7370 (m) cc_final: 0.7079 (p) REVERT: I 68 LYS cc_start: 0.8072 (mttt) cc_final: 0.7790 (mttp) REVERT: K 36 LYS cc_start: 0.8864 (mttt) cc_final: 0.8594 (mttp) REVERT: M 4 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7734 (mtp85) REVERT: M 45 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7688 (mtm180) REVERT: N 43 ASN cc_start: 0.7128 (p0) cc_final: 0.6561 (p0) REVERT: O 93 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8142 (mtpp) REVERT: R 35 ILE cc_start: 0.7611 (mt) cc_final: 0.7363 (mt) REVERT: R 40 ASN cc_start: 0.8093 (m-40) cc_final: 0.7840 (m110) REVERT: T 17 ASP cc_start: 0.6275 (m-30) cc_final: 0.5996 (m-30) REVERT: T 35 VAL cc_start: 0.8695 (t) cc_final: 0.8440 (m) REVERT: U 82 TYR cc_start: 0.6137 (p90) cc_final: 0.5922 (p90) REVERT: Y 48 ASN cc_start: 0.7463 (t0) cc_final: 0.7260 (t0) REVERT: e 1 MET cc_start: 0.1380 (tpt) cc_final: 0.0291 (pmm) REVERT: e 86 MET cc_start: 0.0624 (mmm) cc_final: -0.0066 (mmm) REVERT: f 439 MET cc_start: 0.7005 (mmt) cc_final: 0.6460 (ttt) REVERT: f 462 THR cc_start: 0.7817 (p) cc_final: 0.7473 (p) REVERT: f 497 VAL cc_start: 0.8818 (t) cc_final: 0.8451 (p) REVERT: f 519 ILE cc_start: 0.8640 (tt) cc_final: 0.8377 (tt) REVERT: f 588 GLU cc_start: 0.7623 (mp0) cc_final: 0.7280 (mp0) REVERT: f 591 LEU cc_start: 0.7304 (mt) cc_final: 0.6243 (tp) REVERT: f 592 HIS cc_start: 0.7820 (m-70) cc_final: 0.7464 (m90) REVERT: f 660 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8455 (mtpp) REVERT: f 661 PHE cc_start: 0.8625 (t80) cc_final: 0.8306 (t80) REVERT: f 692 VAL cc_start: 0.7208 (t) cc_final: 0.6528 (p) REVERT: f 715 GLU cc_start: 0.7669 (tp30) cc_final: 0.7356 (tm-30) REVERT: f 716 VAL cc_start: 0.7515 (t) cc_final: 0.7175 (p) REVERT: f 771 ILE cc_start: 0.8232 (tp) cc_final: 0.7922 (tp) REVERT: f 823 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8045 (mttp) REVERT: f 880 PHE cc_start: 0.6698 (p90) cc_final: 0.6387 (p90) REVERT: h 55 VAL cc_start: 0.8429 (t) cc_final: 0.7943 (m) REVERT: h 168 ARG cc_start: 0.7381 (ttp80) cc_final: 0.6500 (ttp-110) REVERT: j 113 LEU cc_start: 0.7525 (tp) cc_final: 0.7293 (tt) REVERT: j 199 ILE cc_start: 0.8099 (mp) cc_final: 0.7514 (tp) REVERT: l 66 VAL cc_start: 0.8793 (t) cc_final: 0.8520 (m) REVERT: l 98 ASP cc_start: 0.7730 (p0) cc_final: 0.7169 (p0) REVERT: n 1 MET cc_start: 0.4158 (tpp) cc_final: 0.3922 (tpt) REVERT: p 48 PHE cc_start: 0.7750 (p90) cc_final: 0.7139 (p90) REVERT: r 42 LEU cc_start: 0.7293 (mt) cc_final: 0.7022 (mm) REVERT: w 90 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7415 (ttm110) outliers start: 20 outliers final: 4 residues processed: 2065 average time/residue: 1.5986 time to fit residues: 5469.5994 Evaluate side-chains 1522 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1518 time to evaluate : 6.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain f residue 861 CYS Chi-restraints excluded: chain j residue 219 THR Chi-restraints excluded: chain x residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 893 optimal weight: 8.9990 chunk 801 optimal weight: 10.0000 chunk 444 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 540 optimal weight: 9.9990 chunk 428 optimal weight: 2.9990 chunk 829 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 504 optimal weight: 0.5980 chunk 617 optimal weight: 6.9990 chunk 960 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 60 GLN B 20 ASN B 85 ASN C 49 GLN C 150 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN L 22 GLN N 34 HIS N 38 GLN ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 ASN O 76 HIS P 36 GLN Q 87 GLN R 15 GLN R 61 ASN S 48 GLN S 70 HIS S 91 GLN T 44 HIS ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS V 45 HIS W 15 ASN X 45 GLN Z 4 GLN f 448 HIS f 478 GLN f 658 GLN f 857 ASN j 23 ASN j 38 HIS j 50 ASN j 189 ASN k 42 ASN k 69 ASN k 76 ASN ** k 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 147 ASN n 52 ASN n 55 HIS n 58 HIS n 63 ASN q 39 ASN ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 7 ASN ** s 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 27 GLN u 37 HIS x 8 GLN x 30 HIS y 63 GLN y 79 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 159795 Z= 0.229 Angle : 0.650 21.029 238503 Z= 0.338 Chirality : 0.038 0.332 30412 Planarity : 0.005 0.109 13162 Dihedral : 22.244 179.989 78608 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.96 % Favored : 91.10 % Rotamer: Outliers : 3.42 % Allowed : 14.64 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.64 (0.10), residues: 6144 helix: -0.92 (0.12), residues: 1675 sheet: -1.94 (0.15), residues: 973 loop : -2.17 (0.09), residues: 3496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 64 HIS 0.028 0.002 HIS S 15 PHE 0.032 0.002 PHE X 26 TYR 0.033 0.002 TYR w 19 ARG 0.012 0.001 ARG P 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1943 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1769 time to evaluate : 6.511 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: 1 29 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6173 (mmmm) REVERT: 3 14 GLU cc_start: 0.7313 (tp30) cc_final: 0.6732 (tp30) REVERT: 3 60 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7654 (mm110) REVERT: B 24 HIS cc_start: 0.7814 (t-170) cc_final: 0.7241 (t-170) REVERT: B 43 ASN cc_start: 0.8194 (t0) cc_final: 0.7721 (t0) REVERT: B 174 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7927 (ttm170) REVERT: B 193 GLU cc_start: 0.5976 (mt-10) cc_final: 0.5716 (mt-10) REVERT: C 126 ASN cc_start: 0.8081 (m-40) cc_final: 0.7839 (m-40) REVERT: D 146 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8616 (m) REVERT: D 176 ASP cc_start: 0.7534 (p0) cc_final: 0.7186 (p0) REVERT: H 116 MET cc_start: 0.4369 (mpp) cc_final: 0.3436 (mtm) REVERT: I 21 THR cc_start: 0.7346 (m) cc_final: 0.7012 (p) REVERT: I 68 LYS cc_start: 0.8349 (mttt) cc_final: 0.8019 (mttp) REVERT: I 103 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8520 (mp) REVERT: J 31 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7472 (mtt-85) REVERT: M 24 MET cc_start: 0.7989 (tpp) cc_final: 0.7641 (ttt) REVERT: M 35 LYS cc_start: 0.8632 (tttt) cc_final: 0.8366 (tttm) REVERT: M 45 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8116 (mtm180) REVERT: N 4 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8105 (tptp) REVERT: N 43 ASN cc_start: 0.7440 (p0) cc_final: 0.6914 (p0) REVERT: O 54 LEU cc_start: 0.8432 (tp) cc_final: 0.8145 (tp) REVERT: O 93 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8288 (mtpt) REVERT: P 35 PHE cc_start: 0.8466 (t80) cc_final: 0.8239 (t80) REVERT: T 39 ASN cc_start: 0.7118 (t0) cc_final: 0.6652 (t0) REVERT: U 80 HIS cc_start: 0.7294 (t-90) cc_final: 0.7034 (t70) REVERT: U 82 TYR cc_start: 0.6754 (p90) cc_final: 0.6511 (p90) REVERT: X 5 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6821 (mt-10) REVERT: c 45 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8390 (Cg_exo) REVERT: c 56 LEU cc_start: 0.8870 (mt) cc_final: 0.8668 (mt) REVERT: e 1 MET cc_start: 0.1789 (tpt) cc_final: 0.0541 (pmm) REVERT: e 86 MET cc_start: 0.0314 (mmm) cc_final: -0.0338 (mmm) REVERT: f 401 ASP cc_start: 0.7903 (t0) cc_final: 0.7621 (t0) REVERT: f 439 MET cc_start: 0.7008 (mmt) cc_final: 0.6642 (ttt) REVERT: f 481 GLU cc_start: 0.8903 (tp30) cc_final: 0.8334 (tp30) REVERT: f 591 LEU cc_start: 0.7252 (mt) cc_final: 0.6651 (mp) REVERT: f 603 TYR cc_start: 0.7939 (p90) cc_final: 0.7502 (p90) REVERT: f 628 ILE cc_start: 0.8396 (tp) cc_final: 0.8079 (tt) REVERT: f 651 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6841 (ttm170) REVERT: f 662 ARG cc_start: 0.7729 (ptm160) cc_final: 0.7324 (mtp-110) REVERT: f 692 VAL cc_start: 0.7433 (t) cc_final: 0.7102 (p) REVERT: f 756 LYS cc_start: 0.8082 (tttp) cc_final: 0.7452 (ttpt) REVERT: f 766 ARG cc_start: 0.8100 (ptp-170) cc_final: 0.7748 (ptt-90) REVERT: f 802 ASP cc_start: 0.6560 (t0) cc_final: 0.6209 (t0) REVERT: f 829 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7208 (mtp85) REVERT: h 33 ASP cc_start: 0.7589 (t0) cc_final: 0.7319 (t0) REVERT: h 36 PHE cc_start: 0.7823 (t80) cc_final: 0.7161 (t80) REVERT: h 139 ASN cc_start: 0.5718 (p0) cc_final: 0.5453 (p0) REVERT: j 99 MET cc_start: 0.7019 (ptp) cc_final: 0.6572 (ptt) REVERT: j 173 LYS cc_start: 0.6908 (mmtt) cc_final: 0.6680 (mmtt) REVERT: j 219 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6292 (t) REVERT: k 88 HIS cc_start: 0.7140 (t-90) cc_final: 0.6911 (t-90) REVERT: l 98 ASP cc_start: 0.7676 (p0) cc_final: 0.7410 (p0) REVERT: l 99 ASN cc_start: 0.8717 (t0) cc_final: 0.8153 (t0) REVERT: n 56 LYS cc_start: 0.6656 (mtmt) cc_final: 0.6226 (mtpt) REVERT: q 22 ILE cc_start: 0.6389 (tp) cc_final: 0.6134 (tp) REVERT: t 74 GLN cc_start: 0.8137 (pm20) cc_final: 0.7753 (pm20) REVERT: w 20 PHE cc_start: 0.4103 (m-10) cc_final: 0.3350 (m-10) outliers start: 174 outliers final: 101 residues processed: 1837 average time/residue: 1.3739 time to fit residues: 4243.0597 Evaluate side-chains 1695 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1588 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 1 residue 29 LYS Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain J residue 9 ASN Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 463 ASP Chi-restraints excluded: chain f residue 465 VAL Chi-restraints excluded: chain f residue 469 VAL Chi-restraints excluded: chain f residue 510 VAL Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 581 VAL Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 651 ARG Chi-restraints excluded: chain f residue 720 ILE Chi-restraints excluded: chain f residue 744 VAL Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 769 SER Chi-restraints excluded: chain f residue 871 VAL Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain j residue 186 VAL Chi-restraints excluded: chain j residue 219 THR Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 120 CYS Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 20 SER Chi-restraints excluded: chain s residue 65 GLU Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 64 SER Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 30 LEU Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 533 optimal weight: 0.1980 chunk 298 optimal weight: 10.0000 chunk 799 optimal weight: 10.0000 chunk 654 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 962 optimal weight: 9.9990 chunk 1039 optimal weight: 0.7980 chunk 857 optimal weight: 20.0000 chunk 954 optimal weight: 20.0000 chunk 328 optimal weight: 9.9990 chunk 772 optimal weight: 10.0000 overall best weight: 6.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 12 GLN B 20 ASN B 116 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 HIS G 18 GLN H 30 GLN I 76 HIS I 136 GLN M 107 ASN O 11 GLN ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN P 55 GLN Q 87 GLN R 31 GLN T 44 HIS T 65 GLN ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN X 45 GLN Y 8 GLN c 42 HIS f 532 HIS ** f 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 101 ASN ** j 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN k 42 ASN k 69 ASN k 76 ASN ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 151 GLN ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN q 39 ASN ** r 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 HIS t 111 GLN w 71 HIS x 44 HIS ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 159795 Z= 0.382 Angle : 0.734 21.524 238503 Z= 0.378 Chirality : 0.039 0.383 30412 Planarity : 0.006 0.115 13162 Dihedral : 22.865 179.824 78607 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.16 % Favored : 88.79 % Rotamer: Outliers : 6.35 % Allowed : 17.55 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.56 (0.10), residues: 6144 helix: -0.86 (0.12), residues: 1738 sheet: -1.70 (0.15), residues: 990 loop : -2.20 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 212 HIS 0.014 0.002 HIS f 402 PHE 0.030 0.003 PHE m 61 TYR 0.030 0.003 TYR Q 83 ARG 0.013 0.001 ARG l 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2240 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1917 time to evaluate : 6.579 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: 1 29 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6982 (mmmm) REVERT: 3 14 GLU cc_start: 0.7623 (tp30) cc_final: 0.7353 (tp30) REVERT: 3 26 MET cc_start: 0.8526 (ppp) cc_final: 0.8183 (ppp) REVERT: B 43 ASN cc_start: 0.8256 (t0) cc_final: 0.7944 (t0) REVERT: B 44 ASN cc_start: 0.8750 (p0) cc_final: 0.8508 (p0) REVERT: B 94 LEU cc_start: 0.9212 (tp) cc_final: 0.8700 (tp) REVERT: B 144 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 174 ARG cc_start: 0.8275 (tpp80) cc_final: 0.8034 (ttm110) REVERT: B 180 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: B 212 TRP cc_start: 0.8493 (p90) cc_final: 0.8125 (p90) REVERT: C 2 ILE cc_start: 0.8437 (pt) cc_final: 0.8222 (mm) REVERT: C 20 VAL cc_start: 0.8255 (t) cc_final: 0.7946 (p) REVERT: C 68 PHE cc_start: 0.8651 (m-80) cc_final: 0.8432 (m-10) REVERT: C 84 LEU cc_start: 0.8744 (mm) cc_final: 0.8506 (mt) REVERT: D 111 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: D 136 GLN cc_start: 0.8132 (tp40) cc_final: 0.7608 (tp40) REVERT: D 145 ASP cc_start: 0.6694 (t70) cc_final: 0.6464 (t70) REVERT: D 152 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6841 (tm-30) REVERT: D 157 LEU cc_start: 0.7588 (tp) cc_final: 0.7388 (tt) REVERT: I 21 THR cc_start: 0.8489 (m) cc_final: 0.8160 (p) REVERT: J 44 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8884 (mmtt) REVERT: K 36 LYS cc_start: 0.9453 (mttt) cc_final: 0.9232 (mttp) REVERT: K 135 ILE cc_start: 0.9038 (mm) cc_final: 0.8687 (mt) REVERT: O 93 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8237 (mtpt) REVERT: O 100 ARG cc_start: 0.6985 (mpt-90) cc_final: 0.6768 (mpt-90) REVERT: P 63 ARG cc_start: 0.7845 (ptt90) cc_final: 0.6897 (ptt90) REVERT: Q 62 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: R 37 THR cc_start: 0.8283 (p) cc_final: 0.7827 (m) REVERT: U 48 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: U 61 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8474 (pp) REVERT: W 45 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8581 (m-10) REVERT: c 46 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8397 (mmtt) REVERT: e 86 MET cc_start: 0.0250 (mmm) cc_final: -0.0446 (mmm) REVERT: f 481 GLU cc_start: 0.8942 (tp30) cc_final: 0.8428 (tp30) REVERT: f 485 HIS cc_start: 0.9025 (m90) cc_final: 0.8755 (m-70) REVERT: f 564 MET cc_start: 0.3287 (ttm) cc_final: 0.2681 (ttm) REVERT: f 571 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7725 (tm-30) REVERT: f 715 GLU cc_start: 0.7729 (tp30) cc_final: 0.7407 (tm-30) REVERT: f 756 LYS cc_start: 0.7825 (tttp) cc_final: 0.7466 (ttpt) REVERT: f 766 ARG cc_start: 0.7865 (ptp-170) cc_final: 0.7612 (ptp90) REVERT: h 36 PHE cc_start: 0.8313 (t80) cc_final: 0.7328 (t80) REVERT: h 139 ASN cc_start: 0.7183 (p0) cc_final: 0.6751 (p0) REVERT: j 30 ILE cc_start: 0.7385 (tp) cc_final: 0.6993 (tt) REVERT: k 13 LYS cc_start: 0.7525 (pttp) cc_final: 0.7230 (pttp) REVERT: k 14 LEU cc_start: 0.8884 (pp) cc_final: 0.8420 (pp) REVERT: k 72 ASN cc_start: 0.8063 (p0) cc_final: 0.7823 (p0) REVERT: k 121 ASN cc_start: 0.8875 (m-40) cc_final: 0.8523 (m-40) REVERT: k 133 ILE cc_start: 0.8695 (mp) cc_final: 0.8346 (mp) REVERT: k 147 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7855 (p0) REVERT: l 14 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5849 (mm-30) REVERT: l 47 LEU cc_start: 0.7966 (pt) cc_final: 0.7699 (pt) REVERT: l 58 GLN cc_start: 0.7413 (mt0) cc_final: 0.7133 (mt0) REVERT: l 98 ASP cc_start: 0.7746 (p0) cc_final: 0.7438 (p0) REVERT: l 171 GLU cc_start: 0.6912 (tt0) cc_final: 0.6678 (tt0) REVERT: m 138 GLU cc_start: 0.2938 (OUTLIER) cc_final: 0.2268 (pm20) REVERT: n 1 MET cc_start: 0.5348 (tpp) cc_final: 0.5075 (tpp) REVERT: n 40 GLU cc_start: 0.6014 (pp20) cc_final: 0.5722 (pp20) REVERT: o 17 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5867 (mtm180) REVERT: o 51 LEU cc_start: 0.7764 (mm) cc_final: 0.7555 (mm) REVERT: p 4 ASP cc_start: 0.7220 (t0) cc_final: 0.6946 (t70) REVERT: w 60 GLN cc_start: 0.7519 (mp10) cc_final: 0.7315 (mp10) REVERT: w 85 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7529 (ttp80) outliers start: 323 outliers final: 190 residues processed: 2037 average time/residue: 1.4987 time to fit residues: 5229.5830 Evaluate side-chains 1897 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1697 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain 3 residue 47 GLN Chi-restraints excluded: chain 3 residue 79 THR Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain P residue 55 GLN Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 25 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 PHE Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 21 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 462 THR Chi-restraints excluded: chain f residue 463 ASP Chi-restraints excluded: chain f residue 500 ILE Chi-restraints excluded: chain f residue 510 VAL Chi-restraints excluded: chain f residue 523 GLU Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 549 LEU Chi-restraints excluded: chain f residue 570 ILE Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 599 CYS Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 653 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 691 ILE Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 835 VAL Chi-restraints excluded: chain f residue 871 VAL Chi-restraints excluded: chain f residue 876 VAL Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 105 THR Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 186 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 69 ASN Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 8 LEU Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 17 ARG Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 89 ASP Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 120 CYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain s residue 103 THR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 81 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 30 LEU Chi-restraints excluded: chain u residue 44 GLU Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 3 GLN Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain w residue 85 ARG Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain z residue 38 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 950 optimal weight: 20.0000 chunk 723 optimal weight: 10.0000 chunk 499 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 459 optimal weight: 8.9990 chunk 646 optimal weight: 1.9990 chunk 965 optimal weight: 3.9990 chunk 1022 optimal weight: 10.0000 chunk 504 optimal weight: 4.9990 chunk 915 optimal weight: 0.0170 chunk 275 optimal weight: 8.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN C 36 GLN E 4 HIS E 26 GLN E 80 GLN F 72 ASN F 87 GLN H 30 GLN I 136 GLN K 38 GLN N 19 GLN P 19 GLN P 36 GLN P 51 GLN P 55 GLN P 58 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Y 8 GLN ** f 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS j 23 ASN ** j 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN k 96 GLN ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 21 HIS q 37 GLN ** r 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 GLN ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 51 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 159795 Z= 0.185 Angle : 0.584 20.233 238503 Z= 0.303 Chirality : 0.033 0.351 30412 Planarity : 0.005 0.111 13162 Dihedral : 22.799 179.112 78606 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.33 % Favored : 89.75 % Rotamer: Outliers : 5.38 % Allowed : 22.42 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.21 (0.10), residues: 6144 helix: -0.44 (0.12), residues: 1742 sheet: -1.39 (0.16), residues: 998 loop : -2.09 (0.10), residues: 3404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP j 22 HIS 0.010 0.001 HIS X 41 PHE 0.033 0.002 PHE Y 52 TYR 0.027 0.002 TYR E 127 ARG 0.009 0.001 ARG k 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2058 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1784 time to evaluate : 6.503 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: 3 26 MET cc_start: 0.8324 (ppp) cc_final: 0.8109 (ppp) REVERT: B 43 ASN cc_start: 0.8204 (t0) cc_final: 0.7960 (t0) REVERT: B 174 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7993 (ttm110) REVERT: C 84 LEU cc_start: 0.8626 (mm) cc_final: 0.8426 (mt) REVERT: D 152 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6942 (tm-30) REVERT: E 29 ARG cc_start: 0.7338 (tmm-80) cc_final: 0.7057 (ttp80) REVERT: F 170 THR cc_start: 0.8927 (m) cc_final: 0.8662 (p) REVERT: I 57 LEU cc_start: 0.8853 (mm) cc_final: 0.8425 (mt) REVERT: J 44 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8793 (mmtt) REVERT: L 47 GLU cc_start: 0.7801 (tp30) cc_final: 0.7599 (tp30) REVERT: M 24 MET cc_start: 0.7932 (tpp) cc_final: 0.7641 (ttt) REVERT: M 35 LYS cc_start: 0.8760 (tttt) cc_final: 0.8378 (tttm) REVERT: M 45 ARG cc_start: 0.8548 (mtm180) cc_final: 0.8331 (mtm180) REVERT: M 106 ASP cc_start: 0.8854 (p0) cc_final: 0.8523 (p0) REVERT: N 34 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7594 (m90) REVERT: N 56 LYS cc_start: 0.8057 (mttt) cc_final: 0.7741 (mttt) REVERT: P 63 ARG cc_start: 0.7603 (ptt90) cc_final: 0.6534 (ptt90) REVERT: Q 39 LEU cc_start: 0.8591 (mp) cc_final: 0.8317 (mt) REVERT: W 45 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8386 (m-10) REVERT: b 25 LYS cc_start: 0.8329 (tmmt) cc_final: 0.8089 (ttpt) REVERT: c 46 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8370 (mmtt) REVERT: d 36 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7906 (ttt-90) REVERT: e 1 MET cc_start: 0.3039 (mmm) cc_final: -0.1478 (pmm) REVERT: e 86 MET cc_start: 0.0346 (mmm) cc_final: -0.0337 (mmm) REVERT: f 481 GLU cc_start: 0.8979 (tp30) cc_final: 0.8606 (tp30) REVERT: f 530 PHE cc_start: 0.8727 (m-10) cc_final: 0.8283 (m-80) REVERT: f 564 MET cc_start: 0.3181 (ttm) cc_final: 0.2554 (ttm) REVERT: f 687 HIS cc_start: 0.5322 (p90) cc_final: 0.4043 (p-80) REVERT: f 756 LYS cc_start: 0.7713 (tttp) cc_final: 0.7297 (ttpt) REVERT: f 766 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7583 (ptp90) REVERT: f 799 GLU cc_start: 0.8049 (mp0) cc_final: 0.7658 (mp0) REVERT: f 802 ASP cc_start: 0.6855 (t0) cc_final: 0.6554 (t0) REVERT: h 36 PHE cc_start: 0.7982 (t80) cc_final: 0.7415 (t80) REVERT: h 139 ASN cc_start: 0.6439 (p0) cc_final: 0.6001 (p0) REVERT: k 13 LYS cc_start: 0.7351 (pttp) cc_final: 0.7143 (pttp) REVERT: k 14 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (pp) REVERT: k 72 ASN cc_start: 0.7874 (p0) cc_final: 0.7647 (p0) REVERT: k 121 ASN cc_start: 0.8557 (m-40) cc_final: 0.8244 (m-40) REVERT: k 133 ILE cc_start: 0.8596 (mp) cc_final: 0.8247 (mp) REVERT: k 146 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6108 (ttt) REVERT: l 47 LEU cc_start: 0.8049 (pt) cc_final: 0.7728 (pt) REVERT: l 62 ARG cc_start: 0.7603 (mtt-85) cc_final: 0.7166 (mtt-85) REVERT: l 98 ASP cc_start: 0.7553 (p0) cc_final: 0.7282 (p0) REVERT: l 99 ASN cc_start: 0.8589 (t0) cc_final: 0.8145 (t0) REVERT: n 1 MET cc_start: 0.5389 (tpp) cc_final: 0.4330 (mmm) REVERT: p 4 ASP cc_start: 0.7155 (t0) cc_final: 0.6952 (t70) REVERT: s 52 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6355 (mt) REVERT: t 85 ARG cc_start: 0.7863 (tmm-80) cc_final: 0.7601 (tpt170) REVERT: w 83 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8066 (tppt) REVERT: w 85 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7459 (ttm-80) REVERT: x 29 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8158 (ttmm) outliers start: 274 outliers final: 169 residues processed: 1894 average time/residue: 1.4445 time to fit residues: 4685.4254 Evaluate side-chains 1838 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1662 time to evaluate : 6.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain 3 residue 67 HIS Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 61 TRP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 34 HIS Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 44 ARG Chi-restraints excluded: chain W residue 45 PHE Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 22 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 523 GLU Chi-restraints excluded: chain f residue 556 GLU Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 693 LEU Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 720 ILE Chi-restraints excluded: chain f residue 744 VAL Chi-restraints excluded: chain f residue 748 VAL Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 842 LEU Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 118 THR Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 186 VAL Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 69 ASN Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 146 MET Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain m residue 115 MET Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 19 VAL Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 20 SER Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 52 ILE Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain s residue 103 THR Chi-restraints excluded: chain t residue 17 LYS Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 81 ILE Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 85 ARG Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 37 ILE Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain y residue 19 VAL Chi-restraints excluded: chain y residue 24 SER Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 851 optimal weight: 7.9990 chunk 580 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 761 optimal weight: 10.0000 chunk 421 optimal weight: 0.0050 chunk 872 optimal weight: 3.9990 chunk 706 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 522 optimal weight: 1.9990 chunk 917 optimal weight: 0.0970 chunk 258 optimal weight: 10.0000 overall best weight: 2.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 115 GLN E 4 HIS E 80 GLN F 72 ASN ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN I 136 GLN J 3 GLN K 38 GLN M 11 ASN M 107 ASN N 38 GLN P 36 GLN P 55 GLN P 58 GLN R 31 GLN T 39 ASN T 45 GLN ** V 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN b 29 GLN f 426 GLN f 485 HIS ** f 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 826 ASN h 68 HIS j 23 ASN ** j 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 119 GLN j 202 ASN k 42 ASN k 69 ASN k 76 ASN k 96 GLN k 121 ASN ** l 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 GLN ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 159795 Z= 0.186 Angle : 0.575 18.966 238503 Z= 0.297 Chirality : 0.032 0.374 30412 Planarity : 0.005 0.112 13162 Dihedral : 22.769 179.849 78605 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.24 % Favored : 88.87 % Rotamer: Outliers : 5.50 % Allowed : 24.09 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.04 (0.10), residues: 6144 helix: -0.29 (0.12), residues: 1728 sheet: -1.21 (0.16), residues: 983 loop : -2.02 (0.10), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP j 22 HIS 0.009 0.001 HIS X 41 PHE 0.030 0.002 PHE j 49 TYR 0.025 0.002 TYR k 49 ARG 0.020 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2040 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1760 time to evaluate : 6.393 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: 1 59 LYS cc_start: 0.7873 (mttp) cc_final: 0.7624 (mppt) REVERT: 2 38 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: B 43 ASN cc_start: 0.8224 (t0) cc_final: 0.7920 (t0) REVERT: B 174 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7903 (ttm110) REVERT: B 180 MET cc_start: 0.8431 (mmp) cc_final: 0.8122 (mmm) REVERT: C 68 PHE cc_start: 0.8521 (m-80) cc_final: 0.8314 (m-10) REVERT: D 136 GLN cc_start: 0.8150 (tp40) cc_final: 0.7745 (tp-100) REVERT: F 170 THR cc_start: 0.9027 (m) cc_final: 0.8792 (p) REVERT: I 21 THR cc_start: 0.8298 (m) cc_final: 0.7959 (p) REVERT: I 31 GLU cc_start: 0.8181 (tp30) cc_final: 0.7785 (tp30) REVERT: I 50 THR cc_start: 0.7840 (p) cc_final: 0.7385 (t) REVERT: I 57 LEU cc_start: 0.8943 (mm) cc_final: 0.8604 (mt) REVERT: J 44 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8834 (mmtt) REVERT: K 141 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8177 (ttpt) REVERT: K 143 GLU cc_start: 0.8270 (pm20) cc_final: 0.7395 (pm20) REVERT: L 47 GLU cc_start: 0.7778 (tp30) cc_final: 0.7369 (tp30) REVERT: L 51 ARG cc_start: 0.8404 (tpp80) cc_final: 0.7846 (tpp80) REVERT: M 24 MET cc_start: 0.7952 (tpp) cc_final: 0.7568 (ttt) REVERT: M 35 LYS cc_start: 0.8753 (tttt) cc_final: 0.8357 (tttm) REVERT: M 45 ARG cc_start: 0.8477 (mtm180) cc_final: 0.8271 (mtm180) REVERT: M 106 ASP cc_start: 0.8919 (p0) cc_final: 0.8579 (p0) REVERT: N 34 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7794 (m90) REVERT: N 56 LYS cc_start: 0.8151 (mttt) cc_final: 0.7778 (mttt) REVERT: O 93 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8054 (mtpp) REVERT: P 32 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7532 (tpt90) REVERT: P 63 ARG cc_start: 0.7586 (ptt90) cc_final: 0.6574 (ptt90) REVERT: Q 2 TYR cc_start: 0.7887 (p90) cc_final: 0.7543 (p90) REVERT: R 24 ILE cc_start: 0.9199 (mm) cc_final: 0.8869 (mt) REVERT: T 25 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8704 (mmmt) REVERT: b 2 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8575 (ttpp) REVERT: c 46 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8364 (mmtt) REVERT: e 1 MET cc_start: 0.3115 (mmm) cc_final: -0.1564 (pmm) REVERT: e 86 MET cc_start: 0.0538 (mmm) cc_final: -0.0246 (mmm) REVERT: f 451 PHE cc_start: 0.8296 (m-80) cc_final: 0.7979 (m-80) REVERT: f 481 GLU cc_start: 0.8995 (tp30) cc_final: 0.8622 (tp30) REVERT: f 490 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: f 530 PHE cc_start: 0.8717 (m-10) cc_final: 0.8239 (m-80) REVERT: f 564 MET cc_start: 0.3250 (ttm) cc_final: 0.1836 (ttm) REVERT: f 756 LYS cc_start: 0.7614 (tttp) cc_final: 0.7410 (pttt) REVERT: f 766 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7713 (ptp90) REVERT: f 799 GLU cc_start: 0.8048 (mp0) cc_final: 0.7740 (mp0) REVERT: f 802 ASP cc_start: 0.6869 (t0) cc_final: 0.6527 (t0) REVERT: h 109 GLU cc_start: 0.7952 (mp0) cc_final: 0.7280 (mt-10) REVERT: h 135 ARG cc_start: 0.7100 (mmm-85) cc_final: 0.6703 (mtp85) REVERT: h 139 ASN cc_start: 0.6437 (p0) cc_final: 0.5054 (p0) REVERT: j 67 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8255 (tt) REVERT: j 136 ARG cc_start: 0.6521 (ttt-90) cc_final: 0.6292 (ptm-80) REVERT: k 72 ASN cc_start: 0.7992 (p0) cc_final: 0.7784 (p0) REVERT: k 133 ILE cc_start: 0.8628 (mp) cc_final: 0.8341 (mp) REVERT: k 147 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7863 (p0) REVERT: l 14 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5389 (mm-30) REVERT: l 47 LEU cc_start: 0.8000 (pt) cc_final: 0.7633 (pt) REVERT: l 62 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.7282 (mtt-85) REVERT: l 72 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7477 (tpp80) REVERT: l 97 LEU cc_start: 0.8148 (tt) cc_final: 0.7789 (tp) REVERT: l 98 ASP cc_start: 0.7552 (p0) cc_final: 0.7142 (p0) REVERT: l 99 ASN cc_start: 0.8566 (t0) cc_final: 0.8127 (t0) REVERT: n 1 MET cc_start: 0.5459 (tpp) cc_final: 0.4344 (mmm) REVERT: p 48 PHE cc_start: 0.8241 (p90) cc_final: 0.7968 (p90) REVERT: t 85 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7631 (tpt170) REVERT: u 14 PHE cc_start: 0.8190 (m-10) cc_final: 0.7953 (m-10) REVERT: w 85 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7444 (ttt90) outliers start: 280 outliers final: 183 residues processed: 1871 average time/residue: 1.3343 time to fit residues: 4259.7357 Evaluate side-chains 1881 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1689 time to evaluate : 6.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 VAL Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 2 residue 38 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain N residue 34 HIS Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain P residue 21 LYS Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 25 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 463 ASP Chi-restraints excluded: chain f residue 490 GLN Chi-restraints excluded: chain f residue 523 GLU Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 556 GLU Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 693 LEU Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 835 VAL Chi-restraints excluded: chain f residue 842 LEU Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain f residue 880 PHE Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 185 THR Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain j residue 186 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 69 ASN Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 143 SER Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 120 CYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 81 ILE Chi-restraints excluded: chain u residue 12 SER Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain w residue 85 ARG Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 37 ILE Chi-restraints excluded: chain x residue 54 ILE Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 344 optimal weight: 5.9990 chunk 920 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 600 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 1023 optimal weight: 20.0000 chunk 849 optimal weight: 6.9990 chunk 473 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 537 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 41 GLN D 115 GLN E 4 HIS F 21 GLN ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 38 GLN M 23 ASN P 36 GLN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN R 61 ASN T 45 GLN ** V 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN Z 4 GLN b 29 GLN f 485 HIS ** f 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 2 GLN h 68 HIS j 23 ASN ** j 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN k 76 ASN k 134 ASN ** l 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 19 ASN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 GLN x 49 ASN ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 159795 Z= 0.231 Angle : 0.597 17.699 238503 Z= 0.307 Chirality : 0.033 0.404 30412 Planarity : 0.005 0.112 13162 Dihedral : 22.820 179.987 78605 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.43 % Favored : 88.61 % Rotamer: Outliers : 6.27 % Allowed : 24.46 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.04 (0.10), residues: 6144 helix: -0.25 (0.12), residues: 1731 sheet: -1.27 (0.16), residues: 1017 loop : -2.02 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP h 17 HIS 0.011 0.001 HIS I 77 PHE 0.030 0.002 PHE S 51 TYR 0.034 0.002 TYR o 6 ARG 0.010 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2075 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1756 time to evaluate : 8.765 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: 1 52 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7075 (mtm-85) REVERT: 1 59 LYS cc_start: 0.7968 (mttp) cc_final: 0.7747 (mppt) REVERT: 3 14 GLU cc_start: 0.7178 (tp30) cc_final: 0.6916 (tp30) REVERT: B 43 ASN cc_start: 0.8318 (t0) cc_final: 0.7901 (t0) REVERT: B 174 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7911 (ttm110) REVERT: B 180 MET cc_start: 0.8477 (mmp) cc_final: 0.8183 (mmm) REVERT: C 68 PHE cc_start: 0.8518 (m-80) cc_final: 0.8075 (m-80) REVERT: D 88 ARG cc_start: 0.7739 (mpt180) cc_final: 0.7473 (mtt90) REVERT: D 146 VAL cc_start: 0.9033 (t) cc_final: 0.8831 (m) REVERT: D 152 GLU cc_start: 0.7102 (pm20) cc_final: 0.6242 (tm-30) REVERT: E 37 MET cc_start: 0.6701 (ttp) cc_final: 0.6014 (ttm) REVERT: I 21 THR cc_start: 0.8455 (m) cc_final: 0.8103 (p) REVERT: I 31 GLU cc_start: 0.8196 (tp30) cc_final: 0.7739 (tp30) REVERT: I 50 THR cc_start: 0.8000 (p) cc_final: 0.7596 (t) REVERT: I 57 LEU cc_start: 0.9054 (mm) cc_final: 0.8805 (mt) REVERT: J 44 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8887 (mmtt) REVERT: K 141 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8075 (ttpt) REVERT: K 143 GLU cc_start: 0.8281 (pm20) cc_final: 0.7585 (pm20) REVERT: L 47 GLU cc_start: 0.7735 (tp30) cc_final: 0.7284 (tp30) REVERT: L 51 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7849 (tpp80) REVERT: M 24 MET cc_start: 0.7822 (tpp) cc_final: 0.7455 (ttt) REVERT: M 35 LYS cc_start: 0.8773 (tttt) cc_final: 0.8421 (tttm) REVERT: M 36 THR cc_start: 0.9180 (t) cc_final: 0.8858 (p) REVERT: M 106 ASP cc_start: 0.8692 (p0) cc_final: 0.8398 (p0) REVERT: N 21 LEU cc_start: 0.8787 (mt) cc_final: 0.8555 (mp) REVERT: N 34 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7755 (m90) REVERT: P 32 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7553 (tpt90) REVERT: P 63 ARG cc_start: 0.7700 (ptt90) cc_final: 0.6905 (ptt90) REVERT: P 91 ARG cc_start: 0.6884 (ptp-170) cc_final: 0.6448 (ptp-170) REVERT: R 24 ILE cc_start: 0.9232 (mm) cc_final: 0.8905 (mt) REVERT: R 37 THR cc_start: 0.8211 (p) cc_final: 0.7815 (m) REVERT: T 25 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8657 (mmmt) REVERT: U 48 MET cc_start: 0.8047 (tpp) cc_final: 0.7536 (tpp) REVERT: W 36 ARG cc_start: 0.8448 (ptm160) cc_final: 0.8213 (ptm160) REVERT: X 31 GLN cc_start: 0.5897 (tm130) cc_final: 0.5304 (tp-100) REVERT: c 46 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8467 (mmtt) REVERT: e 86 MET cc_start: 0.0747 (mmm) cc_final: -0.0019 (mmm) REVERT: f 481 GLU cc_start: 0.9000 (tp30) cc_final: 0.8649 (tp30) REVERT: f 530 PHE cc_start: 0.8694 (m-10) cc_final: 0.8262 (m-80) REVERT: f 564 MET cc_start: 0.3378 (ttm) cc_final: 0.1899 (ttm) REVERT: f 756 LYS cc_start: 0.7767 (tttp) cc_final: 0.7544 (pttt) REVERT: f 766 ARG cc_start: 0.7941 (ptp-170) cc_final: 0.7653 (ptp90) REVERT: f 777 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: f 799 GLU cc_start: 0.8048 (mp0) cc_final: 0.7837 (mp0) REVERT: f 802 ASP cc_start: 0.6922 (t0) cc_final: 0.6602 (t0) REVERT: f 843 GLU cc_start: 0.7387 (tp30) cc_final: 0.7162 (tp30) REVERT: h 36 PHE cc_start: 0.8135 (t80) cc_final: 0.7653 (t80) REVERT: h 109 GLU cc_start: 0.7982 (mp0) cc_final: 0.7328 (mt-10) REVERT: h 135 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6784 (mtp85) REVERT: h 139 ASN cc_start: 0.6479 (p0) cc_final: 0.5381 (p0) REVERT: j 30 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6884 (tt) REVERT: k 72 ASN cc_start: 0.8134 (p0) cc_final: 0.7891 (p0) REVERT: k 133 ILE cc_start: 0.8758 (mp) cc_final: 0.8510 (mp) REVERT: l 27 ILE cc_start: 0.3819 (OUTLIER) cc_final: 0.3205 (mp) REVERT: l 39 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8114 (tm-30) REVERT: l 47 LEU cc_start: 0.8196 (pt) cc_final: 0.7882 (pt) REVERT: l 72 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7529 (tpp80) REVERT: l 98 ASP cc_start: 0.7485 (p0) cc_final: 0.7040 (p0) REVERT: l 99 ASN cc_start: 0.8511 (t0) cc_final: 0.8129 (t0) REVERT: n 1 MET cc_start: 0.5621 (tpp) cc_final: 0.4534 (mmm) REVERT: n 92 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7789 (t) REVERT: p 17 GLN cc_start: 0.8425 (mm110) cc_final: 0.8216 (mm-40) REVERT: p 48 PHE cc_start: 0.8305 (p90) cc_final: 0.8077 (p90) REVERT: t 55 ARG cc_start: 0.6910 (tpm170) cc_final: 0.6683 (tpm170) REVERT: t 85 ARG cc_start: 0.8049 (tmm-80) cc_final: 0.7642 (tpt170) outliers start: 319 outliers final: 234 residues processed: 1879 average time/residue: 1.3765 time to fit residues: 4440.9085 Evaluate side-chains 1934 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1692 time to evaluate : 6.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 VAL Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain 3 residue 79 THR Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain N residue 34 HIS Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 18 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 25 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 71 ILE Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 463 ASP Chi-restraints excluded: chain f residue 498 ASN Chi-restraints excluded: chain f residue 523 GLU Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 556 GLU Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 693 LEU Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 720 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 777 GLU Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 835 VAL Chi-restraints excluded: chain f residue 842 LEU Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain f residue 880 PHE Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 43 THR Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 185 THR Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain j residue 186 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 134 ASN Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 143 SER Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 29 LEU Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain n residue 92 THR Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 35 ILE Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 120 CYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain s residue 103 THR Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 81 ILE Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 54 ILE Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 48 ILE Chi-restraints excluded: chain z residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 986 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 583 optimal weight: 9.9990 chunk 747 optimal weight: 10.0000 chunk 579 optimal weight: 6.9990 chunk 861 optimal weight: 9.9990 chunk 571 optimal weight: 1.9990 chunk 1019 optimal weight: 30.0000 chunk 638 optimal weight: 8.9990 chunk 621 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN E 4 HIS ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN F 21 GLN ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN M 107 ASN N 38 GLN P 36 GLN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN U 49 ASN ** V 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 4 GLN b 29 GLN e 57 ASN ** f 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 485 HIS ** f 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 826 ASN h 68 HIS h 189 HIS j 23 ASN ** j 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** l 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 49 GLN w 66 GLN ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 159795 Z= 0.428 Angle : 0.776 17.916 238503 Z= 0.395 Chirality : 0.041 0.400 30412 Planarity : 0.006 0.114 13162 Dihedral : 23.101 179.335 78605 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.99 % Allowed : 11.83 % Favored : 87.17 % Rotamer: Outliers : 6.98 % Allowed : 24.86 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.47 (0.10), residues: 6144 helix: -0.69 (0.12), residues: 1755 sheet: -1.56 (0.16), residues: 1015 loop : -2.24 (0.10), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 17 HIS 0.074 0.003 HIS E 4 PHE 0.027 0.003 PHE S 51 TYR 0.033 0.003 TYR f 517 ARG 0.014 0.001 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2214 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1859 time to evaluate : 5.987 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: 3 14 GLU cc_start: 0.7655 (tp30) cc_final: 0.7307 (tp30) REVERT: 3 18 LYS cc_start: 0.8382 (mmtm) cc_final: 0.7623 (mmtm) REVERT: B 85 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: B 144 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7892 (mm-30) REVERT: B 174 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7968 (ttm110) REVERT: B 180 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: B 212 TRP cc_start: 0.8741 (p90) cc_final: 0.8505 (p90) REVERT: C 84 LEU cc_start: 0.8659 (mm) cc_final: 0.8407 (mt) REVERT: D 1 MET cc_start: 0.5430 (ppp) cc_final: 0.4665 (ppp) REVERT: D 152 GLU cc_start: 0.7393 (pm20) cc_final: 0.6421 (tm-30) REVERT: E 37 MET cc_start: 0.7051 (ttp) cc_final: 0.6459 (ttm) REVERT: E 68 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7639 (mmmt) REVERT: E 91 ARG cc_start: 0.6535 (mtt90) cc_final: 0.6256 (mtt90) REVERT: E 157 THR cc_start: 0.7588 (t) cc_final: 0.7329 (t) REVERT: F 72 ASN cc_start: 0.8566 (t0) cc_final: 0.8328 (t0) REVERT: H 16 MET cc_start: -0.0646 (mtp) cc_final: -0.0937 (mtp) REVERT: I 21 THR cc_start: 0.8531 (m) cc_final: 0.8235 (p) REVERT: I 41 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7525 (ttpp) REVERT: J 44 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9060 (mmtt) REVERT: K 141 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8237 (ttpp) REVERT: K 143 GLU cc_start: 0.8517 (pm20) cc_final: 0.8245 (pm20) REVERT: M 24 MET cc_start: 0.7971 (tpp) cc_final: 0.7483 (ttt) REVERT: M 35 LYS cc_start: 0.8879 (tttt) cc_final: 0.8560 (tttm) REVERT: M 36 THR cc_start: 0.9231 (t) cc_final: 0.8934 (p) REVERT: N 34 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8312 (m90) REVERT: O 2 ASN cc_start: 0.7622 (t0) cc_final: 0.7400 (t0) REVERT: P 91 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6893 (ptp-170) REVERT: Q 23 GLU cc_start: 0.7419 (tp30) cc_final: 0.7167 (tp30) REVERT: Q 32 THR cc_start: 0.8750 (m) cc_final: 0.8471 (t) REVERT: Q 62 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: Q 86 GLN cc_start: 0.6587 (mt0) cc_final: 0.6226 (mt0) REVERT: R 24 ILE cc_start: 0.9363 (mm) cc_final: 0.9015 (mt) REVERT: T 17 ASP cc_start: 0.6461 (m-30) cc_final: 0.6110 (m-30) REVERT: U 25 LYS cc_start: 0.8788 (mttm) cc_final: 0.8422 (mtmm) REVERT: U 43 ASP cc_start: 0.7517 (p0) cc_final: 0.6674 (p0) REVERT: U 48 MET cc_start: 0.8540 (tpp) cc_final: 0.7641 (tpp) REVERT: U 51 GLN cc_start: 0.7812 (pm20) cc_final: 0.7316 (pp30) REVERT: X 31 GLN cc_start: 0.6572 (tm130) cc_final: 0.5902 (tp-100) REVERT: c 28 LEU cc_start: 0.8256 (tp) cc_final: 0.7841 (tp) REVERT: c 48 MET cc_start: 0.8733 (mmp) cc_final: 0.8245 (mmm) REVERT: e 86 MET cc_start: 0.1174 (mmm) cc_final: 0.0385 (mmm) REVERT: f 409 ASP cc_start: 0.8154 (m-30) cc_final: 0.7936 (t0) REVERT: f 414 THR cc_start: 0.9001 (p) cc_final: 0.8741 (p) REVERT: f 451 PHE cc_start: 0.8255 (m-80) cc_final: 0.7935 (m-80) REVERT: f 481 GLU cc_start: 0.8903 (tp30) cc_final: 0.8593 (tp30) REVERT: f 564 MET cc_start: 0.3643 (ttm) cc_final: 0.2201 (ttm) REVERT: f 661 PHE cc_start: 0.8460 (t80) cc_final: 0.8208 (t80) REVERT: f 681 MET cc_start: 0.0120 (tmm) cc_final: -0.0577 (ttt) REVERT: f 706 ASP cc_start: 0.8429 (t70) cc_final: 0.8213 (t0) REVERT: f 756 LYS cc_start: 0.7866 (tttp) cc_final: 0.7484 (ttpt) REVERT: f 766 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7543 (ptp90) REVERT: f 777 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: f 802 ASP cc_start: 0.6872 (t0) cc_final: 0.6316 (t0) REVERT: f 804 PHE cc_start: 0.7087 (m-10) cc_final: 0.6630 (m-10) REVERT: f 872 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8722 (mpp80) REVERT: h 139 ASN cc_start: 0.7854 (p0) cc_final: 0.7307 (p0) REVERT: j 30 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6586 (tt) REVERT: k 68 ARG cc_start: 0.7382 (ptp-170) cc_final: 0.6974 (ptp-170) REVERT: k 72 ASN cc_start: 0.8153 (p0) cc_final: 0.7922 (p0) REVERT: k 147 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7907 (p0) REVERT: l 14 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5847 (mm-30) REVERT: l 58 GLN cc_start: 0.7510 (mt0) cc_final: 0.6974 (mt0) REVERT: l 98 ASP cc_start: 0.7569 (p0) cc_final: 0.7139 (p0) REVERT: l 99 ASN cc_start: 0.8667 (t0) cc_final: 0.8334 (t0) REVERT: m 21 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7359 (mm) REVERT: n 1 MET cc_start: 0.5937 (tpp) cc_final: 0.4864 (mmm) REVERT: n 40 GLU cc_start: 0.6682 (pp20) cc_final: 0.6367 (pp20) REVERT: q 51 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.6971 (p90) REVERT: w 17 ASP cc_start: 0.6295 (p0) cc_final: 0.6078 (p0) REVERT: z 43 MET cc_start: 0.6195 (mmt) cc_final: 0.5768 (mmt) REVERT: z 77 ARG cc_start: 0.7517 (mtt90) cc_final: 0.6916 (mtm-85) outliers start: 355 outliers final: 260 residues processed: 1995 average time/residue: 1.3053 time to fit residues: 4458.5022 Evaluate side-chains 2053 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1782 time to evaluate : 6.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain 3 residue 67 HIS Chi-restraints excluded: chain 3 residue 79 THR Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 34 HIS Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain P residue 21 LYS Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 18 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 52 ASN Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 71 ILE Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 22 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 462 THR Chi-restraints excluded: chain f residue 463 ASP Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 570 ILE Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 599 CYS Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 641 VAL Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 693 LEU Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 769 SER Chi-restraints excluded: chain f residue 777 GLU Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 835 VAL Chi-restraints excluded: chain f residue 842 LEU Chi-restraints excluded: chain f residue 876 VAL Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain f residue 880 PHE Chi-restraints excluded: chain h residue 37 LYS Chi-restraints excluded: chain h residue 43 THR Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 185 THR Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 143 SER Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 90 VAL Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 74 LEU Chi-restraints excluded: chain o residue 34 LEU Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 35 ILE Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 89 ASP Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 51 PHE Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain r residue 18 ILE Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain s residue 103 THR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 81 ILE Chi-restraints excluded: chain t residue 89 LEU Chi-restraints excluded: chain u residue 12 SER Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 44 GLU Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain w residue 81 ARG Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 47 ASP Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 9 HIS Chi-restraints excluded: chain y residue 24 SER Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 630 optimal weight: 7.9990 chunk 407 optimal weight: 10.0000 chunk 609 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 648 optimal weight: 0.9990 chunk 694 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 801 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN F 21 GLN ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN I 136 GLN N 38 GLN P 36 GLN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN T 45 GLN U 49 ASN ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 485 HIS ** f 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 792 GLN h 68 HIS h 189 HIS j 93 HIS k 42 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 134 ASN ** m 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 63 ASN ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 159795 Z= 0.399 Angle : 0.727 17.184 238503 Z= 0.372 Chirality : 0.040 0.484 30412 Planarity : 0.006 0.113 13162 Dihedral : 23.162 179.784 78605 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.69 % Favored : 87.35 % Rotamer: Outliers : 6.58 % Allowed : 27.53 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.54 (0.10), residues: 6144 helix: -0.75 (0.12), residues: 1754 sheet: -1.65 (0.16), residues: 1030 loop : -2.26 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 96 HIS 0.021 0.002 HIS E 4 PHE 0.026 0.003 PHE u 14 TYR 0.044 0.003 TYR f 517 ARG 0.012 0.001 ARG f 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2172 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1837 time to evaluate : 6.432 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: B 17 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8264 (mtpp) REVERT: B 85 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.8007 (m-40) REVERT: B 144 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 174 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7983 (ttm110) REVERT: B 180 MET cc_start: 0.8500 (mmp) cc_final: 0.8237 (mmm) REVERT: D 1 MET cc_start: 0.6218 (ppp) cc_final: 0.5623 (ppp) REVERT: D 136 GLN cc_start: 0.8329 (tp40) cc_final: 0.8121 (tp-100) REVERT: D 146 VAL cc_start: 0.9270 (t) cc_final: 0.9008 (m) REVERT: D 152 GLU cc_start: 0.7354 (pm20) cc_final: 0.6453 (tm-30) REVERT: E 91 ARG cc_start: 0.6683 (mtt90) cc_final: 0.6413 (mtt90) REVERT: F 72 ASN cc_start: 0.8599 (t0) cc_final: 0.8369 (t0) REVERT: H 16 MET cc_start: -0.1005 (mtp) cc_final: -0.1235 (mtp) REVERT: I 21 THR cc_start: 0.8541 (m) cc_final: 0.8235 (p) REVERT: I 31 GLU cc_start: 0.8151 (tp30) cc_final: 0.7877 (tp30) REVERT: I 50 THR cc_start: 0.8424 (p) cc_final: 0.8112 (t) REVERT: J 44 LYS cc_start: 0.9358 (mmmm) cc_final: 0.9082 (mmtt) REVERT: K 77 ILE cc_start: 0.8967 (mp) cc_final: 0.8498 (mt) REVERT: K 141 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8232 (ttpp) REVERT: K 143 GLU cc_start: 0.8441 (pm20) cc_final: 0.8115 (pm20) REVERT: L 47 GLU cc_start: 0.7975 (tp30) cc_final: 0.7613 (tp30) REVERT: M 24 MET cc_start: 0.7897 (tpp) cc_final: 0.7592 (ttt) REVERT: M 35 LYS cc_start: 0.8902 (tttt) cc_final: 0.8581 (tttm) REVERT: M 36 THR cc_start: 0.9226 (t) cc_final: 0.8947 (p) REVERT: M 49 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7060 (mt-10) REVERT: M 106 ASP cc_start: 0.8554 (p0) cc_final: 0.8324 (p0) REVERT: N 8 ILE cc_start: 0.9075 (tt) cc_final: 0.8718 (mt) REVERT: O 75 THR cc_start: 0.8925 (p) cc_final: 0.8657 (m) REVERT: P 32 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7629 (tpt90) REVERT: P 91 ARG cc_start: 0.7126 (ptp-170) cc_final: 0.6755 (ptp-170) REVERT: Q 23 GLU cc_start: 0.7358 (tp30) cc_final: 0.7121 (tp30) REVERT: Q 32 THR cc_start: 0.8668 (m) cc_final: 0.8425 (t) REVERT: R 24 ILE cc_start: 0.9372 (mm) cc_final: 0.8979 (mt) REVERT: S 89 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7262 (tm-30) REVERT: T 25 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8728 (mmmt) REVERT: U 43 ASP cc_start: 0.7585 (p0) cc_final: 0.7226 (p0) REVERT: U 48 MET cc_start: 0.8587 (tpp) cc_final: 0.8074 (tpp) REVERT: U 51 GLN cc_start: 0.7724 (pm20) cc_final: 0.7503 (pp30) REVERT: W 25 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8953 (mmmt) REVERT: b 33 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7558 (mtm180) REVERT: c 28 LEU cc_start: 0.8318 (tp) cc_final: 0.7908 (tp) REVERT: d 36 ARG cc_start: 0.8267 (ttt-90) cc_final: 0.8061 (ttt-90) REVERT: f 409 ASP cc_start: 0.8331 (m-30) cc_final: 0.8099 (t0) REVERT: f 426 GLN cc_start: 0.8142 (pt0) cc_final: 0.7813 (pt0) REVERT: f 432 HIS cc_start: 0.6907 (p90) cc_final: 0.6517 (p90) REVERT: f 451 PHE cc_start: 0.8298 (m-80) cc_final: 0.8012 (m-80) REVERT: f 530 PHE cc_start: 0.9124 (m-80) cc_final: 0.8694 (m-80) REVERT: f 564 MET cc_start: 0.3696 (ttm) cc_final: 0.2202 (ttm) REVERT: f 706 ASP cc_start: 0.8555 (t70) cc_final: 0.8254 (t0) REVERT: f 756 LYS cc_start: 0.7870 (tttp) cc_final: 0.7648 (pttt) REVERT: f 766 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7488 (ptp90) REVERT: f 777 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: f 799 GLU cc_start: 0.8146 (mp0) cc_final: 0.7821 (mp0) REVERT: f 802 ASP cc_start: 0.6854 (t0) cc_final: 0.6233 (t0) REVERT: f 804 PHE cc_start: 0.7120 (m-10) cc_final: 0.6636 (m-10) REVERT: h 36 PHE cc_start: 0.8115 (t80) cc_final: 0.6957 (t80) REVERT: h 139 ASN cc_start: 0.7640 (p0) cc_final: 0.6965 (p0) REVERT: j 67 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8298 (tt) REVERT: k 72 ASN cc_start: 0.8098 (p0) cc_final: 0.7894 (p0) REVERT: k 147 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7727 (p0) REVERT: l 25 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6694 (tmm-80) REVERT: l 30 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7043 (pttt) REVERT: l 47 LEU cc_start: 0.8287 (pt) cc_final: 0.8078 (pp) REVERT: l 72 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7642 (tpp80) REVERT: l 98 ASP cc_start: 0.7290 (p0) cc_final: 0.7054 (p0) REVERT: l 99 ASN cc_start: 0.8601 (t0) cc_final: 0.8262 (t0) REVERT: m 21 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7396 (mm) REVERT: n 21 MET cc_start: 0.6441 (mmm) cc_final: 0.6144 (mmm) REVERT: p 79 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7988 (mtm110) REVERT: q 51 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6706 (p90) REVERT: q 124 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4805 (ttpp) REVERT: r 24 GLU cc_start: 0.6003 (pp20) cc_final: 0.5765 (pp20) REVERT: t 72 ASN cc_start: 0.8298 (p0) cc_final: 0.8038 (p0) REVERT: u 76 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5563 (ptm160) REVERT: x 71 SER cc_start: 0.8207 (m) cc_final: 0.7796 (t) outliers start: 335 outliers final: 267 residues processed: 1968 average time/residue: 1.5271 time to fit residues: 5202.8654 Evaluate side-chains 2049 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1768 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain 3 residue 67 HIS Chi-restraints excluded: chain 3 residue 79 THR Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain P residue 21 LYS Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 18 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 25 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 71 ILE Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain c residue 30 HIS Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 485 HIS Chi-restraints excluded: chain f residue 498 ASN Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 693 LEU Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 769 SER Chi-restraints excluded: chain f residue 777 GLU Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 792 GLN Chi-restraints excluded: chain f residue 835 VAL Chi-restraints excluded: chain f residue 842 LEU Chi-restraints excluded: chain f residue 876 VAL Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain h residue 37 LYS Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 43 THR Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 149 LYS Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 185 THR Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 31 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 134 ASN Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 25 ARG Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 143 SER Chi-restraints excluded: chain l residue 168 THR Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 90 VAL Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain m residue 115 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 35 ILE Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 89 ASP Chi-restraints excluded: chain p residue 105 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 51 PHE Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 120 CYS Chi-restraints excluded: chain q residue 124 LYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 64 GLN Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 73 SER Chi-restraints excluded: chain s residue 103 THR Chi-restraints excluded: chain t residue 3 VAL Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain u residue 12 SER Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 44 GLU Chi-restraints excluded: chain u residue 76 ARG Chi-restraints excluded: chain u residue 84 LEU Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain w residue 100 SER Chi-restraints excluded: chain x residue 19 SER Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 54 ILE Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 66 LEU Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 19 VAL Chi-restraints excluded: chain y residue 24 SER Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 38 THR Chi-restraints excluded: chain z residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 927 optimal weight: 10.0000 chunk 976 optimal weight: 9.9990 chunk 891 optimal weight: 0.9990 chunk 950 optimal weight: 20.0000 chunk 571 optimal weight: 1.9990 chunk 413 optimal weight: 4.9990 chunk 746 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 858 optimal weight: 2.9990 chunk 898 optimal weight: 0.7980 chunk 946 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN D 97 ASN D 115 GLN F 21 GLN ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN O 6 GLN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN T 39 ASN T 45 GLN U 49 ASN U 75 GLN V 56 HIS ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN ** f 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 485 HIS f 498 ASN h 184 ASN j 93 HIS ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 134 ASN l 197 HIS n 63 ASN ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 51 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 159795 Z= 0.163 Angle : 0.609 16.600 238503 Z= 0.313 Chirality : 0.033 0.486 30412 Planarity : 0.005 0.111 13162 Dihedral : 23.100 179.504 78605 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.74 % Favored : 88.36 % Rotamer: Outliers : 4.58 % Allowed : 29.87 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.27 (0.10), residues: 6144 helix: -0.44 (0.12), residues: 1723 sheet: -1.49 (0.16), residues: 1018 loop : -2.14 (0.10), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP j 22 HIS 0.017 0.001 HIS X 41 PHE 0.031 0.002 PHE I 89 TYR 0.031 0.002 TYR k 49 ARG 0.010 0.001 ARG O 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2022 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1789 time to evaluate : 6.357 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: 2 19 LYS cc_start: 0.5375 (mppt) cc_final: 0.5148 (mttp) REVERT: B 17 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: B 144 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 187 CYS cc_start: 0.8514 (p) cc_final: 0.8258 (p) REVERT: D 136 GLN cc_start: 0.8258 (tp40) cc_final: 0.7994 (tp-100) REVERT: D 146 VAL cc_start: 0.9203 (t) cc_final: 0.8950 (m) REVERT: D 152 GLU cc_start: 0.7353 (pm20) cc_final: 0.6472 (tm-30) REVERT: E 25 MET cc_start: 0.6232 (tpp) cc_final: 0.5523 (tpp) REVERT: E 91 ARG cc_start: 0.6383 (mtt90) cc_final: 0.6149 (mtt90) REVERT: H 16 MET cc_start: -0.0521 (mtp) cc_final: -0.0812 (mtp) REVERT: I 21 THR cc_start: 0.8413 (m) cc_final: 0.8152 (p) REVERT: I 31 GLU cc_start: 0.8058 (tp30) cc_final: 0.7790 (tp30) REVERT: I 50 THR cc_start: 0.8010 (p) cc_final: 0.7659 (t) REVERT: I 120 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7821 (mtt90) REVERT: J 44 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9009 (mmtt) REVERT: K 141 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8233 (ttpt) REVERT: K 143 GLU cc_start: 0.8275 (pm20) cc_final: 0.7608 (pm20) REVERT: M 35 LYS cc_start: 0.8892 (tttt) cc_final: 0.8575 (tttm) REVERT: M 36 THR cc_start: 0.9171 (t) cc_final: 0.8904 (p) REVERT: M 106 ASP cc_start: 0.8781 (p0) cc_final: 0.8555 (p0) REVERT: N 8 ILE cc_start: 0.8950 (tt) cc_final: 0.8575 (mt) REVERT: P 31 TYR cc_start: 0.8326 (t80) cc_final: 0.7883 (t80) REVERT: P 32 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7361 (tpt90) REVERT: P 105 PHE cc_start: 0.8607 (t80) cc_final: 0.8349 (t80) REVERT: R 24 ILE cc_start: 0.9226 (mm) cc_final: 0.8880 (mt) REVERT: R 40 ASN cc_start: 0.8265 (m-40) cc_final: 0.7892 (m-40) REVERT: U 35 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6537 (tm-30) REVERT: U 48 MET cc_start: 0.8264 (tpp) cc_final: 0.8012 (mmm) REVERT: U 75 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8073 (tp40) REVERT: X 31 GLN cc_start: 0.6496 (tm130) cc_final: 0.5780 (tp-100) REVERT: b 13 ASN cc_start: 0.8613 (m-40) cc_final: 0.8405 (m-40) REVERT: c 28 LEU cc_start: 0.8293 (tp) cc_final: 0.7908 (tp) REVERT: f 451 PHE cc_start: 0.8349 (m-80) cc_final: 0.8108 (m-80) REVERT: f 530 PHE cc_start: 0.9070 (m-80) cc_final: 0.8519 (m-80) REVERT: f 564 MET cc_start: 0.3596 (ttm) cc_final: 0.2105 (ttm) REVERT: f 706 ASP cc_start: 0.8437 (t70) cc_final: 0.8087 (t0) REVERT: f 756 LYS cc_start: 0.7840 (tttp) cc_final: 0.7596 (pttt) REVERT: f 799 GLU cc_start: 0.7945 (mp0) cc_final: 0.7649 (mp0) REVERT: f 802 ASP cc_start: 0.6929 (t0) cc_final: 0.6610 (t0) REVERT: f 854 GLU cc_start: 0.8371 (mp0) cc_final: 0.8068 (mp0) REVERT: h 99 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8197 (tm-30) REVERT: h 139 ASN cc_start: 0.6750 (p0) cc_final: 0.6012 (p0) REVERT: h 149 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7993 (ttpt) REVERT: h 151 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7175 (tm-30) REVERT: j 22 TRP cc_start: 0.6972 (p-90) cc_final: 0.6473 (p-90) REVERT: j 67 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8269 (tt) REVERT: k 147 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7670 (p0) REVERT: l 30 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6673 (pttp) REVERT: l 62 ARG cc_start: 0.7600 (mpt-90) cc_final: 0.7353 (mpt-90) REVERT: l 72 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7363 (tpp80) REVERT: l 97 LEU cc_start: 0.8240 (tt) cc_final: 0.7718 (tp) REVERT: l 98 ASP cc_start: 0.7337 (p0) cc_final: 0.7093 (p0) REVERT: l 99 ASN cc_start: 0.8446 (t0) cc_final: 0.8216 (t0) REVERT: m 21 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7142 (mm) REVERT: o 56 MET cc_start: 0.2036 (mmm) cc_final: 0.1561 (mmm) REVERT: p 4 ASP cc_start: 0.7768 (t0) cc_final: 0.7521 (t70) REVERT: p 17 GLN cc_start: 0.8640 (mm110) cc_final: 0.8401 (mm-40) REVERT: q 51 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6607 (p90) REVERT: t 85 ARG cc_start: 0.8067 (tmm-80) cc_final: 0.7661 (tpt170) REVERT: w 70 PRO cc_start: 0.8730 (Cg_endo) cc_final: 0.8391 (Cg_exo) REVERT: w 93 ILE cc_start: 0.8408 (mp) cc_final: 0.8196 (mp) REVERT: x 71 SER cc_start: 0.8010 (m) cc_final: 0.7728 (t) REVERT: x 76 ARG cc_start: 0.6926 (ptm-80) cc_final: 0.6463 (ttp80) REVERT: y 12 LYS cc_start: 0.7835 (tttm) cc_final: 0.7550 (tptp) REVERT: z 10 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5672 (tp) REVERT: z 77 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7070 (mtm-85) outliers start: 233 outliers final: 167 residues processed: 1887 average time/residue: 1.3284 time to fit residues: 4270.8767 Evaluate side-chains 1888 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1711 time to evaluate : 6.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 53 GLN Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 75 GLN Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 483 ILE Chi-restraints excluded: chain f residue 485 HIS Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain h residue 43 THR Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 149 LYS Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 31 SER Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 133 ILE Chi-restraints excluded: chain k residue 134 ASN Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 168 THR Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain m residue 115 MET Chi-restraints excluded: chain n residue 8 PHE Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 51 PHE Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain t residue 114 SER Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain x residue 7 LEU Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 66 LEU Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 19 VAL Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 10 ILE Chi-restraints excluded: chain z residue 11 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 624 optimal weight: 9.9990 chunk 1004 optimal weight: 9.9990 chunk 613 optimal weight: 30.0000 chunk 476 optimal weight: 0.0030 chunk 698 optimal weight: 30.0000 chunk 1054 optimal weight: 4.9990 chunk 970 optimal weight: 0.0000 chunk 839 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 648 optimal weight: 2.9990 chunk 514 optimal weight: 5.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 3 GLN O 6 GLN P 36 GLN P 58 GLN Q 82 HIS ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN U 49 ASN U 75 GLN W 35 HIS ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 4 GLN ** f 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 485 HIS f 826 ASN h 68 HIS j 18 GLN k 42 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 134 ASN ** m 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 58 ASN w 49 GLN ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 159795 Z= 0.209 Angle : 0.623 16.731 238503 Z= 0.319 Chirality : 0.034 0.477 30412 Planarity : 0.005 0.111 13162 Dihedral : 23.043 179.100 78605 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.68 % Favored : 88.46 % Rotamer: Outliers : 4.05 % Allowed : 30.12 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.22 (0.10), residues: 6144 helix: -0.40 (0.12), residues: 1727 sheet: -1.46 (0.16), residues: 1018 loop : -2.10 (0.10), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP j 22 HIS 0.023 0.002 HIS I 77 PHE 0.028 0.002 PHE S 51 TYR 0.034 0.002 TYR l 102 ARG 0.013 0.001 ARG f 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1933 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1727 time to evaluate : 6.063 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: 1 59 LYS cc_start: 0.8461 (mttp) cc_final: 0.8165 (mppt) REVERT: 2 19 LYS cc_start: 0.5469 (mppt) cc_final: 0.5063 (mmtp) REVERT: B 17 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8268 (mtpp) REVERT: B 144 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 136 GLN cc_start: 0.8350 (tp40) cc_final: 0.8066 (tp-100) REVERT: D 146 VAL cc_start: 0.9180 (t) cc_final: 0.8954 (m) REVERT: D 152 GLU cc_start: 0.7460 (pm20) cc_final: 0.6532 (tm-30) REVERT: E 25 MET cc_start: 0.6136 (tpp) cc_final: 0.5614 (tpp) REVERT: E 37 MET cc_start: 0.7046 (tmm) cc_final: 0.6126 (tpp) REVERT: E 91 ARG cc_start: 0.6400 (mtt90) cc_final: 0.6189 (mtt90) REVERT: E 95 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6277 (tmm) REVERT: F 98 LYS cc_start: 0.7961 (tppt) cc_final: 0.7700 (tptp) REVERT: H 16 MET cc_start: -0.0520 (mtp) cc_final: -0.0804 (mtp) REVERT: I 21 THR cc_start: 0.8457 (m) cc_final: 0.8189 (p) REVERT: I 31 GLU cc_start: 0.8082 (tp30) cc_final: 0.7829 (tp30) REVERT: I 50 THR cc_start: 0.8031 (p) cc_final: 0.7652 (t) REVERT: I 103 ILE cc_start: 0.8649 (pt) cc_final: 0.8281 (mt) REVERT: I 120 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7784 (mtt90) REVERT: K 4 ASN cc_start: 0.8278 (p0) cc_final: 0.8055 (p0) REVERT: K 141 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8156 (ttpt) REVERT: K 143 GLU cc_start: 0.8302 (pm20) cc_final: 0.7621 (pm20) REVERT: M 35 LYS cc_start: 0.8819 (tttt) cc_final: 0.8474 (tttm) REVERT: M 49 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6982 (mt-10) REVERT: M 106 ASP cc_start: 0.8774 (p0) cc_final: 0.8572 (p0) REVERT: M 112 TYR cc_start: 0.8353 (m-80) cc_final: 0.8081 (m-80) REVERT: N 8 ILE cc_start: 0.9005 (tt) cc_final: 0.8630 (mt) REVERT: O 75 THR cc_start: 0.8820 (p) cc_final: 0.8580 (m) REVERT: P 31 TYR cc_start: 0.8561 (t80) cc_final: 0.8221 (t80) REVERT: P 32 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7547 (tpt90) REVERT: R 24 ILE cc_start: 0.9196 (mm) cc_final: 0.8863 (mt) REVERT: R 40 ASN cc_start: 0.8296 (m-40) cc_final: 0.8089 (m-40) REVERT: R 68 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7165 (p0) REVERT: U 35 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6668 (tm-30) REVERT: U 43 ASP cc_start: 0.7466 (p0) cc_final: 0.7179 (p0) REVERT: U 51 GLN cc_start: 0.7962 (pp30) cc_final: 0.7505 (tm-30) REVERT: U 75 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: X 31 GLN cc_start: 0.6599 (tm130) cc_final: 0.5819 (tp-100) REVERT: b 6 GLN cc_start: 0.7783 (mt0) cc_final: 0.7532 (mt0) REVERT: c 28 LEU cc_start: 0.8332 (tp) cc_final: 0.7935 (tp) REVERT: f 409 ASP cc_start: 0.8443 (m-30) cc_final: 0.8053 (t0) REVERT: f 530 PHE cc_start: 0.9006 (m-80) cc_final: 0.8412 (m-80) REVERT: f 564 MET cc_start: 0.3722 (ttm) cc_final: 0.2130 (ttm) REVERT: f 661 PHE cc_start: 0.8348 (t80) cc_final: 0.8105 (t80) REVERT: f 706 ASP cc_start: 0.8477 (t70) cc_final: 0.8144 (t0) REVERT: f 756 LYS cc_start: 0.7843 (tttp) cc_final: 0.7619 (pttt) REVERT: f 766 ARG cc_start: 0.7746 (ptp90) cc_final: 0.7401 (mtm110) REVERT: f 799 GLU cc_start: 0.7961 (mp0) cc_final: 0.7676 (mp0) REVERT: f 802 ASP cc_start: 0.6951 (t0) cc_final: 0.6636 (t0) REVERT: f 853 ASN cc_start: 0.7317 (t0) cc_final: 0.7019 (t0) REVERT: f 854 GLU cc_start: 0.8474 (mp0) cc_final: 0.8261 (mp0) REVERT: h 99 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8120 (tm-30) REVERT: h 149 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: j 26 MET cc_start: 0.5214 (mmt) cc_final: 0.4591 (mmt) REVERT: j 67 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8287 (tt) REVERT: k 147 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7662 (p0) REVERT: l 30 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6755 (pttp) REVERT: l 62 ARG cc_start: 0.7524 (mpt-90) cc_final: 0.7290 (mpt-90) REVERT: l 72 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7398 (tpp80) REVERT: l 98 ASP cc_start: 0.7503 (p0) cc_final: 0.7253 (p0) REVERT: m 21 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7205 (mm) REVERT: p 4 ASP cc_start: 0.7832 (t0) cc_final: 0.7443 (t70) REVERT: q 51 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6691 (p90) REVERT: t 56 LEU cc_start: 0.8361 (mt) cc_final: 0.7829 (mt) REVERT: t 85 ARG cc_start: 0.8132 (tmm-80) cc_final: 0.7655 (tpt170) REVERT: u 76 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5269 (ptm160) REVERT: w 70 PRO cc_start: 0.8736 (Cg_endo) cc_final: 0.8404 (Cg_exo) REVERT: x 71 SER cc_start: 0.8062 (m) cc_final: 0.7705 (t) outliers start: 206 outliers final: 172 residues processed: 1817 average time/residue: 1.3375 time to fit residues: 4157.7723 Evaluate side-chains 1881 residues out of total 5089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1697 time to evaluate : 6.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 53 GLN Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 3 residue 22 SER Chi-restraints excluded: chain 3 residue 79 THR Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 9 GLN Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 75 GLN Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain d residue 6 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 20 ASP Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain f residue 437 ASN Chi-restraints excluded: chain f residue 485 HIS Chi-restraints excluded: chain f residue 542 ASP Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 590 THR Chi-restraints excluded: chain f residue 626 VAL Chi-restraints excluded: chain f residue 632 SER Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 690 ASN Chi-restraints excluded: chain f residue 704 ILE Chi-restraints excluded: chain f residue 764 ASP Chi-restraints excluded: chain f residue 768 TYR Chi-restraints excluded: chain f residue 785 MET Chi-restraints excluded: chain f residue 879 VAL Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 43 THR Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 149 LYS Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 190 THR Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain j residue 56 LEU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 135 MET Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain j residue 185 ILE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 31 SER Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 130 THR Chi-restraints excluded: chain k residue 134 ASN Chi-restraints excluded: chain k residue 147 ASN Chi-restraints excluded: chain l residue 30 LYS Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 123 MET Chi-restraints excluded: chain l residue 189 ASP Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain m residue 27 ASN Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 90 VAL Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain m residue 115 MET Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 8 ASP Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 26 PHE Chi-restraints excluded: chain q residue 51 PHE Chi-restraints excluded: chain q residue 99 LEU Chi-restraints excluded: chain r residue 58 ASN Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 32 ILE Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain t residue 57 THR Chi-restraints excluded: chain t residue 114 SER Chi-restraints excluded: chain u residue 21 THR Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain u residue 76 ARG Chi-restraints excluded: chain w residue 80 SER Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 27 PHE Chi-restraints excluded: chain x residue 69 THR Chi-restraints excluded: chain x residue 74 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 19 VAL Chi-restraints excluded: chain y residue 69 ASP Chi-restraints excluded: chain z residue 11 ASP Chi-restraints excluded: chain z residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1058 random chunks: chunk 666 optimal weight: 0.8980 chunk 894 optimal weight: 0.5980 chunk 257 optimal weight: 10.0000 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 840 optimal weight: 10.0000 chunk 351 optimal weight: 0.8980 chunk 863 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 overall best weight: 3.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN P 36 GLN P 58 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN U 49 ASN W 35 HIS ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 4 GLN f 485 HIS h 68 HIS k 42 ASN k 76 ASN ** k 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 63 ASN ** o 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 58 ASN u 19 ASN ** z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089983 restraints weight = 324051.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092642 restraints weight = 98722.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094208 restraints weight = 48643.387| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 159795 Z= 0.255 Angle : 0.636 17.682 238503 Z= 0.325 Chirality : 0.034 0.358 30412 Planarity : 0.005 0.111 13162 Dihedral : 23.034 178.570 78605 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.20 % Favored : 87.91 % Rotamer: Outliers : 4.40 % Allowed : 29.93 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.26 (0.10), residues: 6144 helix: -0.42 (0.12), residues: 1744 sheet: -1.52 (0.16), residues: 1036 loop : -2.13 (0.10), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 96 HIS 0.016 0.002 HIS I 77 PHE 0.030 0.002 PHE k 47 TYR 0.053 0.002 TYR B 61 ARG 0.012 0.001 ARG U 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57035.84 seconds wall clock time: 986 minutes 30.88 seconds (59190.88 seconds total)