Starting phenix.real_space_refine on Sun Feb 25 09:34:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yst_10907/02_2024/6yst_10907_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4643 5.49 5 Mg 253 5.21 5 S 149 5.16 5 Na 2 4.78 5 C 73807 2.51 5 N 27358 2.21 5 O 40633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 8": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d GLU 77": "OE1" <-> "OE2" Residue "d ARG 103": "NH1" <-> "NH2" Residue "d ARG 110": "NH1" <-> "NH2" Residue "d ARG 127": "NH1" <-> "NH2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d ARG 183": "NH1" <-> "NH2" Residue "d GLU 186": "OE1" <-> "OE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "g GLU 47": "OE1" <-> "OE2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g GLU 138": "OE1" <-> "OE2" Residue "i ARG 40": "NH1" <-> "NH2" Residue "i ARG 44": "NH1" <-> "NH2" Residue "i GLU 58": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 121": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "m GLU 46": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o GLU 5": "OE1" <-> "OE2" Residue "o TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s ARG 80": "NH1" <-> "NH2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "u ARG 16": "NH1" <-> "NH2" Residue "u ARG 20": "NH1" <-> "NH2" Residue "u GLU 23": "OE1" <-> "OE2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u ARG 46": "NH1" <-> "NH2" Residue "v ARG 12": "NH1" <-> "NH2" Residue "y GLU 16": "OE1" <-> "OE2" Residue "y ARG 21": "NH1" <-> "NH2" Residue "y ARG 55": "NH1" <-> "NH2" Residue "y ARG 78": "NH1" <-> "NH2" Residue "y ARG 90": "NH1" <-> "NH2" Residue "y ARG 105": "NH1" <-> "NH2" Residue "y ARG 109": "NH1" <-> "NH2" Residue "y ARG 117": "NH1" <-> "NH2" Residue "y ARG 118": "NH1" <-> "NH2" Residue "y ARG 132": "NH1" <-> "NH2" Residue "y ARG 136": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146847 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 647 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 125} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 180 Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p': 6, 'rna2p_pur': 240, 'rna2p_pyr': 123, 'rna3p': 17, 'rna3p_pur': 1426, 'rna3p_pyr': 1091} Link IDs: {'rna2p': 369, 'rna3p': 2533} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 109} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 693 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 9, 'TRANS': 131} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 140 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 1, 'rna2p_pur': 113, 'rna2p_pyr': 72, 'rna3p': 10, 'rna3p_pur': 756, 'rna3p_pyr': 588} Link IDs: {'rna2p': 186, 'rna3p': 1353} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" 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: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" 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: "g" 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: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" 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: "m" 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: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 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: "q" 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: "r" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "s" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" 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: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "v" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 8} Chain: "w" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1631 Classifications: {'RNA': 76} Modifications used: {'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 6, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 12, 'rna3p': 63} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "x" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "y" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1078 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" 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: "6" 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: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Unusual residues: {' MG': 206, ' NA': 1} Classifications: {'undetermined': 207} Link IDs: {None: 206} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Unusual residues: {' MG': 35} Classifications: {'undetermined': 35} Link IDs: {None: 34} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1819 SG CYS 4 11 177.492 102.084 121.979 1.00 72.22 S ATOM 1844 SG CYS 4 14 177.151 104.748 121.732 1.00 71.87 S ATOM 1947 SG CYS 4 27 177.711 102.091 119.145 1.00 73.36 S ATOM 2825 SG CYS 6 18 129.421 96.925 225.787 1.00147.35 S ATOM 2988 SG CYS 6 40 129.916 99.299 222.722 1.00142.68 S Time building chain proxies: 56.30, per 1000 atoms: 0.38 Number of scatterers: 146847 At special positions: 0 Unit cell: (238.96, 261, 244.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 149 16.00 P 4643 15.00 Mg 253 11.99 Na 2 11.00 O 40633 8.00 N 27358 7.00 C 73807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 70.58 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 18 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 40 " Number of angles added : 3 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11228 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 192 helices and 71 sheets defined 38.9% alpha, 17.4% beta 1535 base pairs and 2273 stacking pairs defined. Time for finding SS restraints: 74.96 Creating SS restraints... Processing helix chain '0' and resid 8 through 20 removed outlier: 4.944A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix No H-bonds generated for 'chain '1' and resid 25 through 30' Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.640A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 4.202A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.818A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 51 through 62 removed outlier: 4.601A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.694A pdb=" N LYS 5 8 " --> pdb=" O ASN 5 4 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN 5 9 " --> pdb=" O LEU 5 5 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU 5 14 " --> pdb=" O ALA 5 10 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL 5 15 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 36 through 48 removed outlier: 5.484A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU 5 41 " --> pdb=" O LYS 5 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 65 removed outlier: 3.813A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU 5 65 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 59 through 65' Processing helix chain '5' and resid 93 through 106 removed outlier: 4.021A pdb=" N LYS 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 46 removed outlier: 4.444A pdb=" N THR 6 45 " --> pdb=" O HIS 6 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY 6 46 " --> pdb=" O PRO 6 42 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 41 through 46' Processing helix chain '6' and resid 55 through 64 removed outlier: 5.176A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 7.620A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 130 through 135 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.976A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.713A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.128A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.233A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.763A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.875A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.181A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.345A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.551A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 5.750A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'F' and resid 1 through 20 removed outlier: 3.654A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 3.774A pdb=" N VAL F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) Proline residue: F 28 - end of helix No H-bonds generated for 'chain 'F' and resid 23 through 28' Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.206A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.252A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.758A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 141 through 146 removed outlier: 5.921A pdb=" N VAL F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP F 146 " --> pdb=" O TYR F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 161 through 173 removed outlier: 4.171A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.755A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.680A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 4.852A pdb=" N GLY H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.107A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 69 removed outlier: 4.150A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 78 removed outlier: 7.106A pdb=" N THR H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 78' Processing helix chain 'H' and resid 95 through 105 Processing helix chain 'I' and resid 19 through 24 removed outlier: 4.702A pdb=" N VAL I 23 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.902A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 34 through 40' Processing helix chain 'I' and resid 74 through 79 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 120 through 135 removed outlier: 4.444A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 30 removed outlier: 4.176A pdb=" N GLN I 29 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN I 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.114A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.907A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.511A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 120 Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.599A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.711A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.956A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 5.069A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 5.594A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.735A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.268A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 37 through 58 removed outlier: 4.514A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.209A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.610A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 5.143A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 4.075A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.559A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 4.447A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.708A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.640A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.647A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.216A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.542A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.179A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.805A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.925A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.539A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.930A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.492A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.941A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.547A pdb=" N GLU Y 5 " --> pdb=" O MET Y 1 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 removed outlier: 6.587A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.385A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 removed outlier: 4.038A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.586A pdb=" N LYS b 27 " --> pdb=" O ASN b 23 " (cutoff:3.500A) Proline residue: b 28 - end of helix No H-bonds generated for 'chain 'b' and resid 23 through 28' Processing helix chain 'b' and resid 43 through 61 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 75 through 87 removed outlier: 4.279A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.571A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.588A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.997A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 Processing helix chain 'c' and resid 27 through 46 Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.459A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.697A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.518A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 68 through 82 removed outlier: 5.113A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR d 75 " --> pdb=" O PHE d 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA d 78 " --> pdb=" O TYR d 74 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA d 79 " --> pdb=" O TYR d 75 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.942A pdb=" N ASN d 88 " --> pdb=" O ASN d 84 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 Processing helix chain 'd' and resid 151 through 162 removed outlier: 7.014A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.860A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.740A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.570A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.855A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 157 removed outlier: 4.729A pdb=" N GLY e 157 " --> pdb=" O ALA e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 5.527A pdb=" N GLY e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 Proline residue: f 19 - end of helix removed outlier: 3.826A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.732A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 57 through 69 removed outlier: 4.459A pdb=" N GLU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 110 removed outlier: 4.840A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 removed outlier: 4.616A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 40 through 55 removed outlier: 4.713A pdb=" N ARG i 44 " --> pdb=" O ARG i 40 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N MET i 45 " --> pdb=" O GLU i 41 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL i 46 " --> pdb=" O THR i 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.614A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 90 removed outlier: 3.654A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 4.760A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.415A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 6.715A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.226A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 5.017A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 74 removed outlier: 5.030A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 103 removed outlier: 4.044A pdb=" N SER k 94 " --> pdb=" O PRO k 90 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.108A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 5.156A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 4.076A pdb=" N LEU m 47 " --> pdb=" O LYS m 43 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 43 through 48' Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.191A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 removed outlier: 4.040A pdb=" N LYS n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 21 through 32 removed outlier: 3.556A pdb=" N GLU n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE n 29 " --> pdb=" O GLU n 25 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER n 31 " --> pdb=" O LYS n 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 52 removed outlier: 3.775A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 3 through 14 Processing helix chain 'o' and resid 23 through 42 removed outlier: 4.299A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.662A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.799A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'r' and resid 10 through 16 removed outlier: 3.952A pdb=" N ALA r 14 " --> pdb=" O CYS r 10 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.877A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 4.003A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 24 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.759A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 's' and resid 63 through 68 removed outlier: 4.269A pdb=" N VAL s 66 " --> pdb=" O ASP s 63 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N HIS s 68 " --> pdb=" O MET s 65 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 't' and resid 8 through 40 removed outlier: 4.181A pdb=" N ALA t 16 " --> pdb=" O GLN t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix removed outlier: 4.033A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 3.661A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 26 removed outlier: 6.406A pdb=" N LEU u 15 " --> pdb=" O PHE u 11 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG u 16 " --> pdb=" O ASP u 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG u 17 " --> pdb=" O VAL u 13 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS u 24 " --> pdb=" O ARG u 20 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA u 25 " --> pdb=" O SER u 21 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 36 removed outlier: 4.242A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU u 35 " --> pdb=" O VAL u 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE u 36 " --> pdb=" O ARG u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 56 removed outlier: 4.133A pdb=" N ALA u 56 " --> pdb=" O VAL u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 63 removed outlier: 3.788A pdb=" N GLU u 62 " --> pdb=" O LEU u 59 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN u 63 " --> pdb=" O ALA u 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 16 removed outlier: 6.811A pdb=" N LEU y 15 " --> pdb=" O PRO y 11 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU y 16 " --> pdb=" O ASP y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 16' Processing helix chain 'y' and resid 27 through 33 removed outlier: 3.611A pdb=" N ASN y 31 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS y 32 " --> pdb=" O GLN y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 49 through 60 removed outlier: 5.823A pdb=" N GLU y 54 " --> pdb=" O GLU y 50 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG y 55 " --> pdb=" O TYR y 51 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA y 59 " --> pdb=" O ARG y 55 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER y 60 " --> pdb=" O LEU y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 79 through 100 removed outlier: 4.112A pdb=" N GLU y 85 " --> pdb=" O GLU y 81 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU y 88 " --> pdb=" O ARG y 84 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU y 97 " --> pdb=" O ALA y 93 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR y 100 " --> pdb=" O LYS y 96 " (cutoff:3.500A) Processing helix chain 'y' and resid 111 through 133 removed outlier: 4.817A pdb=" N GLY y 133 " --> pdb=" O LYS y 129 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 removed outlier: 4.502A pdb=" N GLU 0 35 " --> pdb=" O ASP 0 30 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 18 through 24 removed outlier: 6.047A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 21 through 24 removed outlier: 5.472A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 14 through 19 removed outlier: 3.563A pdb=" N ARG 4 19 " --> pdb=" O VAL 4 22 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL 4 22 " --> pdb=" O ARG 4 19 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '5' and resid 22 through 28 removed outlier: 4.280A pdb=" N LEU 5 23 " --> pdb=" O GLU 5 87 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU 5 87 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA 5 25 " --> pdb=" O SER 5 85 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER 5 85 " --> pdb=" O ALA 5 25 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 1 through 4 removed outlier: 3.952A pdb=" N ALA C 1 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 32 through 35 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.755A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 170 through 174 Processing sheet with id= 10, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.902A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.595A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.874A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 79 through 84 removed outlier: 5.994A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 1 through 6 removed outlier: 3.609A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.552A pdb=" N THR E 150 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.711A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 71 through 74 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'G' and resid 7 through 10 removed outlier: 3.810A pdb=" N VAL G 10 " --> pdb=" O ASN G 47 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN G 47 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 15 through 18 removed outlier: 4.240A pdb=" N LYS G 26 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 81 through 88 removed outlier: 3.622A pdb=" N LEU G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 22, first strand: chain 'H' and resid 16 through 21 removed outlier: 4.668A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 79 through 82 removed outlier: 3.509A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN H 133 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 25, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.606A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.125A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.762A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 66 removed outlier: 5.898A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS M 34 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.622A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.550A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA O 51 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA O 37 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER O 91 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.381A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER P 84 " --> pdb=" O GLU P 26 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.793A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.068A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY R 50 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 21 removed outlier: 3.819A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 71 through 78 removed outlier: 3.972A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 37, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.972A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.874A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 81 through 86 removed outlier: 5.196A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG U 93 " --> pdb=" O ILE U 102 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 1 through 5 Processing sheet with id= 41, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.774A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 47 through 50 removed outlier: 3.727A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 44, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.853A pdb=" N ARG X 26 " --> pdb=" O GLY X 14 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 33 through 40 Processing sheet with id= 46, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.438A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 88 through 91 Processing sheet with id= 48, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 49, first strand: chain 'c' and resid 163 through 168 removed outlier: 3.656A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 171 through 174 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.961A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 83 through 87 removed outlier: 4.496A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 39 removed outlier: 4.615A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.700A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 43 through 47 removed outlier: 5.636A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 72 through 77 removed outlier: 3.559A pdb=" N GLU g 73 " --> pdb=" O VAL g 88 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.351A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 73 through 76 removed outlier: 4.092A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.600A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS i 21 " --> pdb=" O ASP i 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.896A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.738A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE j 49 " --> pdb=" O TYR j 65 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 41 through 44 removed outlier: 3.583A pdb=" N GLU k 82 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE k 22 " --> pdb=" O MET k 84 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.430A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG l 82 " --> pdb=" O HIS l 95 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 35 through 41 removed outlier: 5.712A pdb=" N ALA l 47 " --> pdb=" O PRO l 41 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 2 through 6 removed outlier: 3.574A pdb=" N ALA p 22 " --> pdb=" O THR p 3 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 37 through 40 removed outlier: 3.754A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN p 40 " --> pdb=" O GLY p 49 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.777A pdb=" N VAL q 58 " --> pdb=" O GLY q 9 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'q' and resid 55 through 58 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 46 through 51 removed outlier: 4.773A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'y' and resid 17 through 21 removed outlier: 8.519A pdb=" N GLY y 68 " --> pdb=" O ILE y 43 " (cutoff:3.500A) 1815 hydrogen bonds defined for protein. 5343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3867 hydrogen bonds 6084 hydrogen bond angles 0 basepair planarities 1535 basepair parallelities 2273 stacking parallelities Total time for adding SS restraints: 240.87 Time building geometry restraints manager: 75.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 9111 1.24 - 1.38: 47683 1.38 - 1.53: 88152 1.53 - 1.67: 13945 1.67 - 1.82: 268 Bond restraints: 159159 Sorted by residual: bond pdb=" N PRO 6 42 " pdb=" CA PRO 6 42 " ideal model delta sigma weight residual 1.469 1.696 -0.227 1.28e-02 6.10e+03 3.14e+02 bond pdb=" C5 5MU w 54 " pdb=" C6 5MU w 54 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C5 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C GLU p 48 " pdb=" O GLU p 48 " ideal model delta sigma weight residual 1.234 1.090 0.144 1.19e-02 7.06e+03 1.46e+02 bond pdb=" C ASN j 58 " pdb=" O ASN j 58 " ideal model delta sigma weight residual 1.235 1.095 0.141 1.26e-02 6.30e+03 1.24e+02 ... (remaining 159154 not shown) Histogram of bond angle deviations from ideal: 49.82 - 68.64: 1 68.64 - 87.46: 5 87.46 - 106.28: 27094 106.28 - 125.10: 192977 125.10 - 143.92: 17849 Bond angle restraints: 237926 Sorted by residual: angle pdb=" O3' 5MU w 54 " pdb=" P PSU w 55 " pdb=" O1P PSU w 55 " ideal model delta sigma weight residual 108.00 49.82 58.18 3.00e+00 1.11e-01 3.76e+02 angle pdb=" CA PHE 6 44 " pdb=" C PHE 6 44 " pdb=" O PHE 6 44 " ideal model delta sigma weight residual 119.43 98.86 20.57 1.21e+00 6.83e-01 2.89e+02 angle pdb=" C ARG d 72 " pdb=" CA ARG d 72 " pdb=" CB ARG d 72 " ideal model delta sigma weight residual 109.99 143.92 -33.93 2.09e+00 2.29e-01 2.64e+02 angle pdb=" O3' 5MU w 54 " pdb=" P PSU w 55 " pdb=" O5* PSU w 55 " ideal model delta sigma weight residual 104.00 80.99 23.01 1.50e+00 4.44e-01 2.35e+02 angle pdb=" C1' G7M w 46 " pdb=" N9 G7M w 46 " pdb=" C8 G7M w 46 " ideal model delta sigma weight residual 94.96 139.23 -44.27 3.00e+00 1.11e-01 2.18e+02 ... (remaining 237921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 88447 35.74 - 71.47: 11834 71.47 - 107.21: 1400 107.21 - 142.94: 54 142.94 - 178.68: 49 Dihedral angle restraints: 101784 sinusoidal: 84391 harmonic: 17393 Sorted by residual: dihedral pdb=" C ARG d 72 " pdb=" N ARG d 72 " pdb=" CA ARG d 72 " pdb=" CB ARG d 72 " ideal model delta harmonic sigma weight residual -122.60 -156.52 33.92 0 2.50e+00 1.60e-01 1.84e+02 dihedral pdb=" C HIS 3 30 " pdb=" N HIS 3 30 " pdb=" CA HIS 3 30 " pdb=" CB HIS 3 30 " ideal model delta harmonic sigma weight residual -122.60 -147.84 25.24 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" C5' A A 752 " pdb=" C4' A A 752 " pdb=" C3' A A 752 " pdb=" O3' A A 752 " ideal model delta sinusoidal sigma weight residual 147.00 79.91 67.09 1 8.00e+00 1.56e-02 9.16e+01 ... (remaining 101781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 30284 0.249 - 0.497: 27 0.497 - 0.746: 5 0.746 - 0.994: 3 0.994 - 1.243: 2 Chirality restraints: 30321 Sorted by residual: chirality pdb=" CA ARG d 72 " pdb=" N ARG d 72 " pdb=" C ARG d 72 " pdb=" CB ARG d 72 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.86e+01 chirality pdb=" P A a 2 " pdb=" OP1 A a 2 " pdb=" OP2 A a 2 " pdb=" O5' A a 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.29 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA GLU H 76 " pdb=" N GLU H 76 " pdb=" C GLU H 76 " pdb=" CB GLU H 76 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 30318 not shown) Planarity restraints: 12937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " 0.071 2.00e-02 2.50e+03 6.18e-01 8.58e+03 pdb=" C4' 2MG a1516 " 0.455 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " 0.681 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " -0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " -0.662 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " -0.178 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " 0.983 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " 0.207 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " -0.959 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.068 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' 5MC a1407 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.638 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.656 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.170 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 0.990 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.219 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.942 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU w 54 " 0.040 2.00e-02 2.50e+03 5.91e-01 7.87e+03 pdb=" C4' 5MU w 54 " 0.442 2.00e-02 2.50e+03 pdb=" O4' 5MU w 54 " 0.671 2.00e-02 2.50e+03 pdb=" C3' 5MU w 54 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 5MU w 54 " -0.602 2.00e-02 2.50e+03 pdb=" C2' 5MU w 54 " -0.203 2.00e-02 2.50e+03 pdb=" O2' 5MU w 54 " 0.936 2.00e-02 2.50e+03 pdb=" C1' 5MU w 54 " 0.219 2.00e-02 2.50e+03 pdb=" N1 5MU w 54 " -0.906 2.00e-02 2.50e+03 ... (remaining 12934 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 279 2.11 - 2.81: 42288 2.81 - 3.51: 220877 3.51 - 4.20: 489332 4.20 - 4.90: 656511 Nonbonded interactions: 1409287 Sorted by model distance: nonbonded pdb=" OP2 G A1455 " pdb="MG MG A3071 " model vdw 1.417 2.170 nonbonded pdb=" P G A1455 " pdb="MG MG A3071 " model vdw 1.505 2.530 nonbonded pdb=" O2' UR3 a1498 " pdb=" OP2 A a1499 " model vdw 1.521 2.440 nonbonded pdb=" OP2 A A2821 " pdb=" NE2 HIS N 3 " model vdw 1.524 2.520 nonbonded pdb=" OP1 U A2022 " pdb="MG MG A3169 " model vdw 1.534 2.170 ... (remaining 1409282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 11.200 Check model and map are aligned: 1.610 Set scattering table: 0.990 Process input model: 569.080 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.340 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 590.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.282 159159 Z= 0.469 Angle : 0.880 58.181 237926 Z= 0.453 Chirality : 0.047 1.243 30321 Planarity : 0.018 0.618 12937 Dihedral : 24.399 178.679 90556 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.47 % Favored : 86.11 % Rotamer: Outliers : 0.48 % Allowed : 9.41 % Favored : 90.11 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.09), residues: 5999 helix: -2.35 (0.09), residues: 1950 sheet: -3.04 (0.13), residues: 1014 loop : -3.54 (0.09), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 212 HIS 0.010 0.001 HIS 3 30 PHE 0.067 0.002 PHE 6 43 TYR 0.018 0.002 TYR S 38 ARG 0.011 0.001 ARG L 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1516 time to evaluate : 6.246 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: 0 56 LYS cc_start: 0.5434 (tptt) cc_final: 0.5153 (pttm) REVERT: 1 26 LYS cc_start: 0.8038 (mttt) cc_final: 0.7821 (mttt) REVERT: 4 35 GLN cc_start: 0.9062 (mp10) cc_final: 0.8197 (mp10) REVERT: 6 25 ARG cc_start: 0.8394 (tpp80) cc_final: 0.7832 (tpp80) REVERT: 6 47 LYS cc_start: 0.7388 (mtpp) cc_final: 0.7065 (pttm) REVERT: 6 59 ARG cc_start: 0.7745 (mpp80) cc_final: 0.7478 (mpt-90) REVERT: C 123 ILE cc_start: 0.9094 (mm) cc_final: 0.8696 (mm) REVERT: F 37 MET cc_start: 0.8032 (mpp) cc_final: 0.7772 (mpp) REVERT: F 41 GLU cc_start: 0.8299 (pm20) cc_final: 0.7811 (pm20) REVERT: F 93 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8146 (mm-30) REVERT: G 123 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7581 (tm-30) REVERT: G 148 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7905 (ttt-90) REVERT: G 176 LYS cc_start: 0.7635 (mptt) cc_final: 0.6363 (tmtt) REVERT: H 4 ILE cc_start: 0.7436 (tp) cc_final: 0.7156 (tp) REVERT: H 35 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7134 (mttt) REVERT: J 106 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8568 (tppp) REVERT: L 27 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8725 (pp) REVERT: L 93 ASN cc_start: 0.7494 (p0) cc_final: 0.7134 (t0) REVERT: N 42 LYS cc_start: 0.9003 (mttm) cc_final: 0.8775 (mttt) REVERT: N 114 GLU cc_start: 0.7568 (pm20) cc_final: 0.7013 (pm20) REVERT: N 116 VAL cc_start: 0.8652 (m) cc_final: 0.7997 (m) REVERT: P 19 PHE cc_start: 0.8726 (p90) cc_final: 0.8481 (p90) REVERT: P 26 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7336 (tm-30) REVERT: P 49 ILE cc_start: 0.9000 (mt) cc_final: 0.8774 (mt) REVERT: Q 93 ILE cc_start: 0.9115 (mm) cc_final: 0.8777 (mm) REVERT: Q 101 ASP cc_start: 0.7487 (t0) cc_final: 0.7265 (t0) REVERT: R 27 ILE cc_start: 0.8510 (mm) cc_final: 0.8301 (mt) REVERT: R 83 TYR cc_start: 0.8378 (t80) cc_final: 0.8157 (t80) REVERT: T 73 ARG cc_start: 0.7358 (mtt90) cc_final: 0.7071 (ttm170) REVERT: X 73 ARG cc_start: 0.6438 (mtm110) cc_final: 0.6235 (mtp180) REVERT: Y 2 LYS cc_start: 0.7974 (pptt) cc_final: 0.7324 (pttt) REVERT: Y 60 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7280 (mmmm) REVERT: Z 2 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7601 (ptpp) REVERT: b 26 MET cc_start: 0.8563 (mmm) cc_final: 0.8153 (mmt) REVERT: b 62 ARG cc_start: 0.7522 (tpp80) cc_final: 0.6582 (mmm160) REVERT: b 88 GLN cc_start: 0.5544 (mp10) cc_final: 0.5094 (mp10) REVERT: b 117 GLU cc_start: 0.6932 (pt0) cc_final: 0.6424 (tt0) REVERT: b 176 ASN cc_start: 0.7300 (m110) cc_final: 0.6949 (m110) REVERT: c 7 ASN cc_start: 0.8145 (t0) cc_final: 0.7741 (m-40) REVERT: c 149 LYS cc_start: 0.6959 (tttt) cc_final: 0.6643 (tmtt) REVERT: d 50 TYR cc_start: 0.7001 (t80) cc_final: 0.6618 (t80) REVERT: d 58 GLN cc_start: 0.7100 (mm110) cc_final: 0.6888 (mm-40) REVERT: d 173 ASP cc_start: 0.7720 (t0) cc_final: 0.7259 (m-30) REVERT: e 59 ILE cc_start: 0.9075 (mt) cc_final: 0.8850 (mm) REVERT: e 64 GLU cc_start: 0.8001 (pt0) cc_final: 0.7579 (pt0) REVERT: f 13 ASP cc_start: 0.7932 (p0) cc_final: 0.7448 (p0) REVERT: f 59 TYR cc_start: 0.7012 (m-80) cc_final: 0.6472 (m-80) REVERT: f 68 GLN cc_start: 0.7092 (mt0) cc_final: 0.6891 (mt0) REVERT: h 13 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8887 (mp) REVERT: h 59 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6538 (tm-30) REVERT: h 72 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7550 (tm-30) REVERT: h 87 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7449 (mtp85) REVERT: i 102 PHE cc_start: 0.5368 (m-10) cc_final: 0.5089 (m-80) REVERT: i 123 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8257 (mmm-85) REVERT: j 66 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6599 (tm-30) REVERT: j 73 LEU cc_start: 0.6761 (tt) cc_final: 0.6373 (tp) REVERT: j 88 MET cc_start: 0.7093 (tmm) cc_final: 0.6541 (tmm) REVERT: k 28 ASN cc_start: 0.8602 (t0) cc_final: 0.8294 (t0) REVERT: l 8 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7417 (mtp-110) REVERT: m 26 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8543 (tppt) REVERT: m 30 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8242 (mttt) REVERT: m 68 LEU cc_start: 0.7833 (tp) cc_final: 0.7358 (tp) REVERT: m 80 MET cc_start: 0.8349 (mtt) cc_final: 0.8099 (mtt) REVERT: o 36 ASN cc_start: 0.9122 (m-40) cc_final: 0.8625 (m110) REVERT: o 76 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7627 (mtm180) REVERT: o 77 TYR cc_start: 0.8483 (t80) cc_final: 0.8014 (t80) REVERT: p 31 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.6912 (ttp-170) REVERT: p 38 PHE cc_start: 0.7812 (p90) cc_final: 0.7583 (p90) REVERT: p 47 GLU cc_start: 0.4138 (OUTLIER) cc_final: 0.3577 (tt0) REVERT: r 24 ASP cc_start: 0.8028 (t0) cc_final: 0.7491 (t70) REVERT: s 16 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7915 (pttt) REVERT: s 31 ARG cc_start: 0.6602 (ttp80) cc_final: 0.5646 (ttp-170) REVERT: t 53 MET cc_start: 0.8180 (ppp) cc_final: 0.7823 (ppp) REVERT: u 16 ARG cc_start: 0.7653 (ttp80) cc_final: 0.6898 (ptp90) REVERT: u 54 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7061 (ptt180) REVERT: y 51 TYR cc_start: 0.5642 (t80) cc_final: 0.3870 (t80) REVERT: y 125 LYS cc_start: 0.8486 (tppt) cc_final: 0.8251 (tppt) outliers start: 23 outliers final: 11 residues processed: 1531 average time/residue: 1.4635 time to fit residues: 3773.2817 Evaluate side-chains 1263 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1249 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain p residue 48 GLU Chi-restraints excluded: chain t residue 7 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 9.9990 chunk 795 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 536 optimal weight: 2.9990 chunk 425 optimal weight: 20.0000 chunk 822 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 500 optimal weight: 6.9990 chunk 612 optimal weight: 5.9990 chunk 953 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 HIS ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 48 GLN 6 61 ASN 6 65 ASN C 52 HIS C 85 ASN C 89 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 136 GLN L 99 ASN N 16 HIS ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 58 GLN R 18 GLN R 87 GLN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Z 19 HIS b 145 ASN c 40 GLN c 138 GLN d 125 ASN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN l 72 ASN m 11 HIS ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN n 43 ASN o 41 HIS o 45 HIS p 18 GLN ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN s 42 ASN s 55 GLN s 68 HIS t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 7 HIS y 23 GLN y 28 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 159159 Z= 0.292 Angle : 0.748 33.312 237926 Z= 0.391 Chirality : 0.040 0.589 30321 Planarity : 0.006 0.133 12937 Dihedral : 24.945 179.979 79136 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.77 % Favored : 89.08 % Rotamer: Outliers : 3.72 % Allowed : 17.26 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.10), residues: 5999 helix: -1.22 (0.11), residues: 1961 sheet: -2.69 (0.14), residues: 1004 loop : -3.06 (0.10), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 212 HIS 0.014 0.001 HIS 6 41 PHE 0.025 0.002 PHE F 174 TYR 0.026 0.002 TYR y 51 ARG 0.011 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1342 time to evaluate : 6.391 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: 0 36 LYS cc_start: 0.8458 (mptt) cc_final: 0.8212 (mtmm) REVERT: 0 56 LYS cc_start: 0.5580 (tptt) cc_final: 0.5370 (pttp) REVERT: 2 44 VAL cc_start: 0.7997 (p) cc_final: 0.7717 (p) REVERT: 4 35 GLN cc_start: 0.9045 (mp10) cc_final: 0.8236 (mp10) REVERT: 6 47 LYS cc_start: 0.7392 (mtpp) cc_final: 0.7014 (pttm) REVERT: 6 59 ARG cc_start: 0.7653 (mpp80) cc_final: 0.7416 (mpt-90) REVERT: C 123 ILE cc_start: 0.9082 (mm) cc_final: 0.8700 (mm) REVERT: E 24 ASN cc_start: 0.8762 (t0) cc_final: 0.8431 (t0) REVERT: F 93 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8012 (mm-30) REVERT: G 123 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7743 (tm-30) REVERT: G 148 ARG cc_start: 0.8026 (ttt-90) cc_final: 0.7760 (ttt-90) REVERT: G 176 LYS cc_start: 0.7526 (mptt) cc_final: 0.6301 (tmtt) REVERT: H 35 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7051 (mttt) REVERT: J 106 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8551 (tppp) REVERT: L 27 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8619 (pp) REVERT: L 93 ASN cc_start: 0.7541 (p0) cc_final: 0.7180 (p0) REVERT: N 42 LYS cc_start: 0.8989 (mttm) cc_final: 0.8768 (mttt) REVERT: N 114 GLU cc_start: 0.7479 (pm20) cc_final: 0.7015 (pm20) REVERT: O 89 ASP cc_start: 0.7612 (p0) cc_final: 0.7368 (p0) REVERT: P 26 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7427 (tm-30) REVERT: R 27 ILE cc_start: 0.8400 (mm) cc_final: 0.8162 (mt) REVERT: R 68 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7572 (mtp180) REVERT: R 83 TYR cc_start: 0.8328 (t80) cc_final: 0.8106 (t80) REVERT: U 35 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8358 (t) REVERT: X 15 ASN cc_start: 0.8837 (m110) cc_final: 0.8525 (m110) REVERT: Y 2 LYS cc_start: 0.8052 (pptt) cc_final: 0.7331 (pttt) REVERT: Y 12 GLU cc_start: 0.7189 (pp20) cc_final: 0.6499 (pm20) REVERT: Y 17 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7910 (tm-30) REVERT: b 26 MET cc_start: 0.8499 (mmm) cc_final: 0.8068 (mmt) REVERT: b 62 ARG cc_start: 0.7490 (tpp80) cc_final: 0.6565 (mmm160) REVERT: b 88 GLN cc_start: 0.5395 (mp10) cc_final: 0.4857 (mp10) REVERT: b 117 GLU cc_start: 0.6908 (pt0) cc_final: 0.6413 (tt0) REVERT: b 168 GLU cc_start: 0.6457 (mp0) cc_final: 0.6224 (mp0) REVERT: b 176 ASN cc_start: 0.7356 (m110) cc_final: 0.6999 (m110) REVERT: c 7 ASN cc_start: 0.8107 (t0) cc_final: 0.7788 (m110) REVERT: c 20 THR cc_start: 0.7107 (p) cc_final: 0.6485 (t) REVERT: c 149 LYS cc_start: 0.6792 (tttt) cc_final: 0.6477 (tmtt) REVERT: d 50 TYR cc_start: 0.6988 (t80) cc_final: 0.6590 (t80) REVERT: d 72 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7309 (mtp-110) REVERT: d 173 ASP cc_start: 0.7728 (t0) cc_final: 0.7258 (m-30) REVERT: e 59 ILE cc_start: 0.9068 (mt) cc_final: 0.8811 (mm) REVERT: e 67 ARG cc_start: 0.7385 (mpt-90) cc_final: 0.7106 (mmt-90) REVERT: e 155 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6203 (tttp) REVERT: f 65 GLU cc_start: 0.7658 (tt0) cc_final: 0.6960 (tm-30) REVERT: g 47 GLU cc_start: 0.7667 (tp30) cc_final: 0.7007 (pp20) REVERT: g 100 MET cc_start: 0.7276 (mtt) cc_final: 0.6905 (mtp) REVERT: h 59 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6466 (tm-30) REVERT: h 72 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7509 (tm-30) REVERT: h 75 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: i 102 PHE cc_start: 0.5431 (m-10) cc_final: 0.5118 (m-80) REVERT: i 123 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8263 (mmm-85) REVERT: j 73 LEU cc_start: 0.6818 (tt) cc_final: 0.6386 (tp) REVERT: j 88 MET cc_start: 0.7204 (tmm) cc_final: 0.6682 (tmm) REVERT: k 100 ASN cc_start: 0.8239 (t0) cc_final: 0.8036 (t0) REVERT: l 8 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7501 (mtp-110) REVERT: m 26 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8510 (tmtt) REVERT: m 68 LEU cc_start: 0.7892 (tp) cc_final: 0.7564 (tp) REVERT: m 80 MET cc_start: 0.8146 (mtt) cc_final: 0.7890 (mtt) REVERT: n 13 VAL cc_start: 0.7736 (m) cc_final: 0.7531 (t) REVERT: n 86 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7865 (tm-30) REVERT: o 36 ASN cc_start: 0.9115 (m-40) cc_final: 0.8625 (m110) REVERT: o 77 TYR cc_start: 0.8462 (t80) cc_final: 0.8087 (t80) REVERT: p 17 TYR cc_start: 0.8006 (m-80) cc_final: 0.7771 (m-80) REVERT: p 47 GLU cc_start: 0.3524 (OUTLIER) cc_final: 0.2585 (tt0) REVERT: r 24 ASP cc_start: 0.7936 (t0) cc_final: 0.7376 (t0) REVERT: s 16 LYS cc_start: 0.8373 (mtpp) cc_final: 0.7901 (pttt) REVERT: s 31 ARG cc_start: 0.6577 (ttp80) cc_final: 0.5801 (ttp-170) REVERT: s 70 LEU cc_start: 0.8437 (mp) cc_final: 0.7911 (mp) REVERT: s 72 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: t 53 MET cc_start: 0.8208 (ppp) cc_final: 0.7878 (ppp) REVERT: u 12 ASP cc_start: 0.6781 (p0) cc_final: 0.6462 (p0) REVERT: u 16 ARG cc_start: 0.7750 (ttp80) cc_final: 0.6970 (ptp90) REVERT: u 54 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7054 (ptt180) outliers start: 177 outliers final: 118 residues processed: 1418 average time/residue: 1.3531 time to fit residues: 3287.1106 Evaluate side-chains 1357 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1233 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 45 ASN Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 chunk 793 optimal weight: 10.0000 chunk 649 optimal weight: 30.0000 chunk 263 optimal weight: 20.0000 chunk 955 optimal weight: 7.9990 chunk 1031 optimal weight: 40.0000 chunk 850 optimal weight: 8.9990 chunk 947 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 766 optimal weight: 50.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN C 259 ASN D 32 ASN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 136 GLN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN c 138 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN m 11 HIS ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 159159 Z= 0.355 Angle : 0.764 33.700 237926 Z= 0.397 Chirality : 0.042 0.584 30321 Planarity : 0.006 0.135 12937 Dihedral : 24.849 179.489 79124 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.35 % Favored : 87.48 % Rotamer: Outliers : 5.30 % Allowed : 19.89 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.10), residues: 5999 helix: -0.79 (0.11), residues: 1940 sheet: -2.46 (0.14), residues: 1013 loop : -2.88 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 166 HIS 0.007 0.001 HIS C 141 PHE 0.022 0.002 PHE d 71 TYR 0.025 0.002 TYR c 41 ARG 0.006 0.001 ARG 0 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1271 time to evaluate : 6.287 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: 0 56 LYS cc_start: 0.5562 (tptt) cc_final: 0.5209 (pttm) REVERT: 2 44 VAL cc_start: 0.7899 (p) cc_final: 0.7651 (p) REVERT: 4 35 GLN cc_start: 0.9049 (mp10) cc_final: 0.8184 (mp10) REVERT: 6 47 LYS cc_start: 0.7467 (mtpp) cc_final: 0.7095 (pttm) REVERT: 6 59 ARG cc_start: 0.7578 (mpp80) cc_final: 0.7337 (mpt-90) REVERT: C 123 ILE cc_start: 0.9121 (mm) cc_final: 0.8765 (mm) REVERT: E 24 ASN cc_start: 0.8835 (t0) cc_final: 0.8580 (t0) REVERT: E 91 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7181 (t70) REVERT: F 93 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8032 (mm-30) REVERT: G 123 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7689 (tt0) REVERT: G 148 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7798 (ttt-90) REVERT: G 176 LYS cc_start: 0.7476 (mptt) cc_final: 0.6276 (tmtt) REVERT: H 35 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7070 (mttt) REVERT: J 54 ILE cc_start: 0.9101 (mt) cc_final: 0.8884 (mt) REVERT: J 106 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8557 (tppp) REVERT: L 27 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8653 (pp) REVERT: L 93 ASN cc_start: 0.7585 (p0) cc_final: 0.7381 (p0) REVERT: N 42 LYS cc_start: 0.9011 (mttm) cc_final: 0.8783 (mttt) REVERT: P 26 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7422 (tm-30) REVERT: R 83 TYR cc_start: 0.8347 (t80) cc_final: 0.8089 (t80) REVERT: V 69 GLU cc_start: 0.7059 (mp0) cc_final: 0.6833 (mp0) REVERT: X 15 ASN cc_start: 0.8835 (m110) cc_final: 0.8528 (m-40) REVERT: X 67 LEU cc_start: 0.8936 (mt) cc_final: 0.8708 (tt) REVERT: X 77 TYR cc_start: 0.6966 (p90) cc_final: 0.6523 (p90) REVERT: Y 2 LYS cc_start: 0.7965 (pptt) cc_final: 0.7238 (pttt) REVERT: Y 13 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: Y 49 ASP cc_start: 0.7842 (t0) cc_final: 0.7467 (t0) REVERT: b 62 ARG cc_start: 0.7432 (tpp80) cc_final: 0.6425 (mmm160) REVERT: b 176 ASN cc_start: 0.7374 (m110) cc_final: 0.7020 (m110) REVERT: c 7 ASN cc_start: 0.8230 (t0) cc_final: 0.7829 (m-40) REVERT: c 20 THR cc_start: 0.7191 (p) cc_final: 0.6501 (t) REVERT: c 149 LYS cc_start: 0.6855 (tttt) cc_final: 0.6535 (tmtt) REVERT: d 50 TYR cc_start: 0.6937 (t80) cc_final: 0.6545 (t80) REVERT: d 72 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7204 (mtp-110) REVERT: d 173 ASP cc_start: 0.7830 (t0) cc_final: 0.7294 (m-30) REVERT: d 205 LYS cc_start: 0.7553 (tptm) cc_final: 0.7227 (mttm) REVERT: e 12 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7572 (mt-10) REVERT: e 67 ARG cc_start: 0.7495 (mpt-90) cc_final: 0.7128 (mpt-90) REVERT: f 25 TYR cc_start: 0.8290 (m-80) cc_final: 0.7589 (m-80) REVERT: g 47 GLU cc_start: 0.7712 (tp30) cc_final: 0.7066 (pp20) REVERT: h 59 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6524 (tm-30) REVERT: h 72 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7547 (tm-30) REVERT: h 75 GLN cc_start: 0.8341 (mp10) cc_final: 0.8121 (mt0) REVERT: h 87 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7742 (mtp85) REVERT: h 127 TYR cc_start: 0.8493 (m-10) cc_final: 0.8246 (m-80) REVERT: i 102 PHE cc_start: 0.5421 (m-10) cc_final: 0.5114 (m-80) REVERT: i 123 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8254 (mmm-85) REVERT: j 73 LEU cc_start: 0.6733 (tt) cc_final: 0.6372 (tp) REVERT: j 88 MET cc_start: 0.7166 (tmm) cc_final: 0.6632 (tmm) REVERT: l 8 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7488 (mtp-110) REVERT: m 26 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8505 (tmtt) REVERT: m 68 LEU cc_start: 0.7824 (tp) cc_final: 0.7473 (tp) REVERT: m 80 MET cc_start: 0.8153 (mtt) cc_final: 0.7908 (mtt) REVERT: n 13 VAL cc_start: 0.7615 (m) cc_final: 0.7394 (t) REVERT: n 86 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7810 (tm-30) REVERT: o 36 ASN cc_start: 0.9132 (m-40) cc_final: 0.8637 (m110) REVERT: o 77 TYR cc_start: 0.8464 (t80) cc_final: 0.8051 (t80) REVERT: p 17 TYR cc_start: 0.8085 (m-80) cc_final: 0.7813 (m-80) REVERT: p 47 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2549 (tt0) REVERT: q 5 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.6024 (ttp-170) REVERT: r 38 ILE cc_start: 0.9081 (mp) cc_final: 0.8814 (mp) REVERT: s 16 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7893 (pttt) REVERT: s 31 ARG cc_start: 0.6642 (ttp80) cc_final: 0.5762 (ttp-170) REVERT: s 70 LEU cc_start: 0.8417 (mp) cc_final: 0.7915 (mp) REVERT: s 72 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: t 53 MET cc_start: 0.8215 (ppp) cc_final: 0.7867 (ppp) REVERT: u 12 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6439 (p0) REVERT: u 16 ARG cc_start: 0.7903 (ttp80) cc_final: 0.6915 (ptp-110) REVERT: u 54 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7189 (ptt180) outliers start: 252 outliers final: 180 residues processed: 1393 average time/residue: 1.2584 time to fit residues: 3028.8190 Evaluate side-chains 1397 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1209 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 24 GLU Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 53 GLN Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 20.0000 chunk 718 optimal weight: 20.0000 chunk 495 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 641 optimal weight: 10.0000 chunk 958 optimal weight: 5.9990 chunk 1014 optimal weight: 30.0000 chunk 500 optimal weight: 7.9990 chunk 908 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN c 138 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 ASN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 159159 Z= 0.284 Angle : 0.719 32.944 237926 Z= 0.377 Chirality : 0.039 0.573 30321 Planarity : 0.006 0.130 12937 Dihedral : 24.779 179.769 79124 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.57 % Favored : 89.30 % Rotamer: Outliers : 5.81 % Allowed : 21.00 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.10), residues: 5999 helix: -0.52 (0.11), residues: 1960 sheet: -2.35 (0.14), residues: 1046 loop : -2.69 (0.10), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 166 HIS 0.007 0.001 HIS C 141 PHE 0.024 0.002 PHE i 19 TYR 0.030 0.002 TYR H 25 ARG 0.008 0.000 ARG 0 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1279 time to evaluate : 6.342 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: 0 56 LYS cc_start: 0.5547 (tptt) cc_final: 0.5239 (pttm) REVERT: 2 44 VAL cc_start: 0.7819 (p) cc_final: 0.7598 (p) REVERT: 4 35 GLN cc_start: 0.9041 (mp10) cc_final: 0.8175 (mp10) REVERT: 6 9 TYR cc_start: 0.5849 (t80) cc_final: 0.5509 (t80) REVERT: 6 47 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7082 (pttm) REVERT: E 24 ASN cc_start: 0.8838 (t0) cc_final: 0.8578 (t0) REVERT: E 91 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7198 (t70) REVERT: F 144 LYS cc_start: 0.8147 (mttt) cc_final: 0.7160 (pptt) REVERT: G 68 ARG cc_start: 0.8611 (tmt170) cc_final: 0.8366 (tmt170) REVERT: G 123 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7726 (tm-30) REVERT: G 148 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.7690 (ttt-90) REVERT: G 176 LYS cc_start: 0.7384 (mptt) cc_final: 0.6214 (tmtt) REVERT: H 18 GLN cc_start: 0.5639 (tp-100) cc_final: 0.5208 (mp10) REVERT: H 35 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7079 (mttt) REVERT: J 95 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7163 (mtm110) REVERT: J 106 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8543 (tppp) REVERT: K 56 ASP cc_start: 0.8425 (m-30) cc_final: 0.8075 (m-30) REVERT: L 27 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8673 (pp) REVERT: L 93 ASN cc_start: 0.7563 (p0) cc_final: 0.7356 (p0) REVERT: N 42 LYS cc_start: 0.8998 (mttm) cc_final: 0.8746 (mttt) REVERT: N 114 GLU cc_start: 0.7763 (pm20) cc_final: 0.7562 (pm20) REVERT: O 43 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7958 (p0) REVERT: P 26 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7385 (tm-30) REVERT: R 83 TYR cc_start: 0.8311 (t80) cc_final: 0.8009 (t80) REVERT: X 15 ASN cc_start: 0.8849 (m110) cc_final: 0.8519 (m-40) REVERT: Y 2 LYS cc_start: 0.7964 (pptt) cc_final: 0.7210 (pttt) REVERT: Y 12 GLU cc_start: 0.7066 (pm20) cc_final: 0.6660 (pm20) REVERT: b 62 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6291 (mmm160) REVERT: b 77 GLU cc_start: 0.6458 (mp0) cc_final: 0.6167 (mp0) REVERT: b 117 GLU cc_start: 0.6897 (pt0) cc_final: 0.6433 (tt0) REVERT: b 168 GLU cc_start: 0.6337 (mp0) cc_final: 0.5864 (mp0) REVERT: c 7 ASN cc_start: 0.8187 (t0) cc_final: 0.7793 (m-40) REVERT: c 149 LYS cc_start: 0.6763 (tttt) cc_final: 0.6483 (tmtt) REVERT: d 50 TYR cc_start: 0.7003 (t80) cc_final: 0.6604 (t80) REVERT: e 60 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7690 (tp-100) REVERT: e 155 LYS cc_start: 0.6849 (ttpp) cc_final: 0.6019 (tttp) REVERT: f 25 TYR cc_start: 0.8218 (m-80) cc_final: 0.7666 (m-80) REVERT: g 47 GLU cc_start: 0.7569 (tp30) cc_final: 0.7021 (pp20) REVERT: g 142 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6849 (tpt90) REVERT: h 59 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6503 (tm-30) REVERT: h 72 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7496 (tm-30) REVERT: i 102 PHE cc_start: 0.5388 (m-10) cc_final: 0.5081 (m-80) REVERT: i 123 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8288 (mmm-85) REVERT: j 73 LEU cc_start: 0.6708 (tt) cc_final: 0.6345 (tp) REVERT: j 88 MET cc_start: 0.7163 (tmm) cc_final: 0.6664 (tmm) REVERT: l 8 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7445 (mtp-110) REVERT: m 26 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8335 (tptt) REVERT: m 30 LYS cc_start: 0.8243 (pttm) cc_final: 0.7834 (mttt) REVERT: m 68 LEU cc_start: 0.7834 (tp) cc_final: 0.7371 (tp) REVERT: m 80 MET cc_start: 0.8268 (mtt) cc_final: 0.8020 (mtt) REVERT: n 32 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5408 (t0) REVERT: n 86 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7800 (tm-30) REVERT: o 36 ASN cc_start: 0.9120 (m-40) cc_final: 0.8614 (m110) REVERT: o 77 TYR cc_start: 0.8418 (t80) cc_final: 0.8067 (t80) REVERT: p 17 TYR cc_start: 0.8061 (m-80) cc_final: 0.7738 (m-80) REVERT: q 5 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5867 (ttp-170) REVERT: q 38 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8138 (mtmt) REVERT: s 16 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7829 (pttt) REVERT: s 31 ARG cc_start: 0.6843 (ttp80) cc_final: 0.5730 (ttp-170) REVERT: s 40 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: s 70 LEU cc_start: 0.8455 (mp) cc_final: 0.7868 (mp) REVERT: s 72 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: t 7 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7691 (ptpt) REVERT: t 53 MET cc_start: 0.8338 (ppp) cc_final: 0.8017 (ppp) REVERT: u 12 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6352 (p0) REVERT: u 16 ARG cc_start: 0.7760 (ttp80) cc_final: 0.6863 (ptp90) REVERT: u 54 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7196 (ptt180) REVERT: y 94 MET cc_start: 0.8418 (ptm) cc_final: 0.8143 (ptm) outliers start: 276 outliers final: 195 residues processed: 1417 average time/residue: 1.3800 time to fit residues: 3399.0499 Evaluate side-chains 1408 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1204 time to evaluate : 6.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 40 PHE Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain y residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 20.0000 chunk 576 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 755 optimal weight: 20.0000 chunk 418 optimal weight: 9.9990 chunk 866 optimal weight: 20.0000 chunk 701 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 518 optimal weight: 2.9990 chunk 910 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 136 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN P 2 ASN c 138 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN l 72 ASN ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN s 68 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 159159 Z= 0.255 Angle : 0.699 32.425 237926 Z= 0.368 Chirality : 0.038 0.558 30321 Planarity : 0.006 0.129 12937 Dihedral : 24.713 178.989 79120 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.59 % Favored : 89.30 % Rotamer: Outliers : 5.74 % Allowed : 22.62 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.60 (0.10), residues: 5999 helix: -0.31 (0.12), residues: 1972 sheet: -2.17 (0.15), residues: 1025 loop : -2.59 (0.11), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 166 HIS 0.006 0.001 HIS C 141 PHE 0.035 0.002 PHE i 19 TYR 0.030 0.002 TYR H 25 ARG 0.011 0.000 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1270 time to evaluate : 6.318 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: 2 44 VAL cc_start: 0.7767 (p) cc_final: 0.7552 (p) REVERT: 4 35 GLN cc_start: 0.8977 (mp10) cc_final: 0.8172 (mp10) REVERT: 6 47 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7054 (pttm) REVERT: C 123 ILE cc_start: 0.9045 (mm) cc_final: 0.8636 (mm) REVERT: E 24 ASN cc_start: 0.8831 (t0) cc_final: 0.8563 (t0) REVERT: E 91 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7351 (t70) REVERT: F 144 LYS cc_start: 0.8131 (mttt) cc_final: 0.7139 (pptt) REVERT: G 123 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7710 (tm-30) REVERT: G 148 ARG cc_start: 0.7946 (ttt-90) cc_final: 0.7693 (ttt-90) REVERT: G 176 LYS cc_start: 0.7360 (mptt) cc_final: 0.6172 (tmtt) REVERT: H 35 LYS cc_start: 0.7339 (mmtt) cc_final: 0.7005 (mttt) REVERT: J 106 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8540 (tppp) REVERT: L 27 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8660 (pp) REVERT: L 93 ASN cc_start: 0.7622 (p0) cc_final: 0.7412 (p0) REVERT: M 31 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6289 (p90) REVERT: M 110 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: N 42 LYS cc_start: 0.8990 (mttm) cc_final: 0.8735 (mttt) REVERT: P 26 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7363 (tm-30) REVERT: Q 96 ASP cc_start: 0.8338 (t0) cc_final: 0.7739 (m-30) REVERT: R 83 TYR cc_start: 0.8330 (t80) cc_final: 0.8043 (t80) REVERT: X 15 ASN cc_start: 0.8885 (m110) cc_final: 0.8587 (m110) REVERT: X 67 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8677 (tt) REVERT: X 77 TYR cc_start: 0.6944 (p90) cc_final: 0.6362 (p90) REVERT: Y 2 LYS cc_start: 0.7828 (pptt) cc_final: 0.6993 (pttt) REVERT: Y 49 ASP cc_start: 0.7734 (t70) cc_final: 0.7306 (t0) REVERT: b 26 MET cc_start: 0.8441 (mmm) cc_final: 0.8081 (mmt) REVERT: b 39 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6875 (tp) REVERT: b 62 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6211 (mmm160) REVERT: b 77 GLU cc_start: 0.6675 (mp0) cc_final: 0.6464 (mp0) REVERT: b 169 HIS cc_start: 0.7880 (p90) cc_final: 0.7627 (p90) REVERT: c 7 ASN cc_start: 0.8238 (t0) cc_final: 0.7820 (m-40) REVERT: c 149 LYS cc_start: 0.6789 (tttt) cc_final: 0.6514 (tmtt) REVERT: d 50 TYR cc_start: 0.7000 (t80) cc_final: 0.6612 (t80) REVERT: e 155 LYS cc_start: 0.6757 (ttpp) cc_final: 0.6015 (tttp) REVERT: f 91 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: g 47 GLU cc_start: 0.7521 (tp30) cc_final: 0.6991 (pp20) REVERT: g 59 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6187 (pm20) REVERT: g 142 ARG cc_start: 0.7275 (mtm110) cc_final: 0.6605 (mmm160) REVERT: h 42 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7565 (tm-30) REVERT: h 59 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6529 (tm-30) REVERT: h 72 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7431 (tm-30) REVERT: i 102 PHE cc_start: 0.5332 (m-10) cc_final: 0.4925 (m-80) REVERT: i 123 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8307 (mmm-85) REVERT: j 65 TYR cc_start: 0.8332 (m-80) cc_final: 0.8082 (m-80) REVERT: j 73 LEU cc_start: 0.6692 (tt) cc_final: 0.6348 (tp) REVERT: j 88 MET cc_start: 0.7105 (tmm) cc_final: 0.6615 (tmm) REVERT: l 8 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7417 (mtp-110) REVERT: m 26 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8300 (tptt) REVERT: m 30 LYS cc_start: 0.8231 (pttm) cc_final: 0.7799 (mttt) REVERT: m 68 LEU cc_start: 0.7815 (tp) cc_final: 0.7432 (tp) REVERT: m 80 MET cc_start: 0.8220 (mtt) cc_final: 0.7964 (mtt) REVERT: n 32 ASP cc_start: 0.6173 (OUTLIER) cc_final: 0.5519 (t0) REVERT: o 36 ASN cc_start: 0.9074 (m-40) cc_final: 0.8550 (m110) REVERT: o 77 TYR cc_start: 0.8346 (t80) cc_final: 0.7987 (t80) REVERT: q 5 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5842 (ttp-170) REVERT: q 38 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8213 (mtmt) REVERT: s 6 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7838 (ttmt) REVERT: s 16 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7813 (pttt) REVERT: s 31 ARG cc_start: 0.6963 (ttp80) cc_final: 0.5811 (ttp-170) REVERT: s 40 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6116 (m-10) REVERT: s 43 MET cc_start: 0.6845 (ptp) cc_final: 0.6340 (ttt) REVERT: s 70 LEU cc_start: 0.8515 (mp) cc_final: 0.7916 (mp) REVERT: s 72 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: t 2 ASN cc_start: 0.6300 (t0) cc_final: 0.5982 (t0) REVERT: t 53 MET cc_start: 0.8422 (ppp) cc_final: 0.8114 (ppp) REVERT: u 12 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6291 (p0) REVERT: u 16 ARG cc_start: 0.7750 (ttp80) cc_final: 0.6864 (ptp90) REVERT: u 54 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7236 (ptt180) REVERT: y 94 MET cc_start: 0.8449 (ptm) cc_final: 0.8222 (ptm) outliers start: 273 outliers final: 207 residues processed: 1409 average time/residue: 1.3200 time to fit residues: 3187.5908 Evaluate side-chains 1416 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1197 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 19 PHE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 119 LYS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 40 PHE Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 20.0000 chunk 913 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 595 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 1015 optimal weight: 0.0870 chunk 843 optimal weight: 30.0000 chunk 470 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 533 optimal weight: 20.0000 overall best weight: 12.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 48 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 ASN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 159159 Z= 0.433 Angle : 0.803 34.352 237926 Z= 0.414 Chirality : 0.044 0.578 30321 Planarity : 0.007 0.136 12937 Dihedral : 24.725 179.767 79116 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.34 % Favored : 87.53 % Rotamer: Outliers : 6.67 % Allowed : 23.51 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 5999 helix: -0.46 (0.11), residues: 1960 sheet: -2.17 (0.15), residues: 1017 loop : -2.60 (0.10), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 166 HIS 0.008 0.001 HIS 6 41 PHE 0.029 0.002 PHE i 19 TYR 0.037 0.003 TYR c 41 ARG 0.011 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1518 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1201 time to evaluate : 6.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 56 LYS cc_start: 0.5653 (tptt) cc_final: 0.5328 (pttm) REVERT: 6 47 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7113 (pttm) REVERT: C 179 GLU cc_start: 0.8170 (tt0) cc_final: 0.7730 (tt0) REVERT: E 91 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7177 (t70) REVERT: F 86 CYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6402 (t) REVERT: G 123 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7750 (tm-30) REVERT: G 176 LYS cc_start: 0.7462 (mptt) cc_final: 0.6253 (tmtt) REVERT: H 35 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6928 (mttt) REVERT: J 106 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8558 (tppp) REVERT: L 27 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8772 (pp) REVERT: L 93 ASN cc_start: 0.7645 (p0) cc_final: 0.7424 (p0) REVERT: N 42 LYS cc_start: 0.9033 (mttm) cc_final: 0.8797 (mttt) REVERT: P 26 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7389 (tm-30) REVERT: P 65 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7764 (p0) REVERT: R 83 TYR cc_start: 0.8325 (t80) cc_final: 0.8062 (t80) REVERT: V 48 MET cc_start: 0.7362 (tpt) cc_final: 0.7149 (tpt) REVERT: X 15 ASN cc_start: 0.8852 (m110) cc_final: 0.8579 (m110) REVERT: X 67 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8647 (tt) REVERT: Y 2 LYS cc_start: 0.7966 (pptt) cc_final: 0.7154 (pttt) REVERT: b 39 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7037 (tp) REVERT: b 62 ARG cc_start: 0.7390 (tpp80) cc_final: 0.6334 (mmm160) REVERT: b 117 GLU cc_start: 0.6871 (pt0) cc_final: 0.6409 (pt0) REVERT: b 176 ASN cc_start: 0.7266 (m110) cc_final: 0.6917 (m110) REVERT: c 7 ASN cc_start: 0.8248 (t0) cc_final: 0.7844 (m-40) REVERT: c 149 LYS cc_start: 0.6849 (tttt) cc_final: 0.6566 (tmtt) REVERT: d 50 TYR cc_start: 0.7063 (t80) cc_final: 0.6677 (t80) REVERT: d 71 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6307 (p90) REVERT: d 72 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7227 (mtp-110) REVERT: e 105 ILE cc_start: 0.8892 (mm) cc_final: 0.8579 (tt) REVERT: e 155 LYS cc_start: 0.6856 (ttpp) cc_final: 0.6045 (tttp) REVERT: f 25 TYR cc_start: 0.8274 (m-80) cc_final: 0.7560 (m-80) REVERT: g 47 GLU cc_start: 0.7552 (tp30) cc_final: 0.7006 (pp20) REVERT: g 59 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: g 142 ARG cc_start: 0.7339 (mtm110) cc_final: 0.6610 (mmm160) REVERT: h 59 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6551 (tm-30) REVERT: h 72 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7498 (tm-30) REVERT: i 102 PHE cc_start: 0.5492 (m-10) cc_final: 0.5188 (m-80) REVERT: i 123 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8288 (mmm-85) REVERT: j 73 LEU cc_start: 0.6705 (tt) cc_final: 0.6345 (tp) REVERT: j 88 MET cc_start: 0.7169 (tmm) cc_final: 0.6611 (tmm) REVERT: l 8 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7492 (mtp-110) REVERT: l 39 THR cc_start: 0.8256 (t) cc_final: 0.7940 (m) REVERT: m 26 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8542 (tmtt) REVERT: m 68 LEU cc_start: 0.7840 (tp) cc_final: 0.7588 (tp) REVERT: m 80 MET cc_start: 0.8267 (mtt) cc_final: 0.7985 (mtt) REVERT: n 13 VAL cc_start: 0.7453 (m) cc_final: 0.7125 (t) REVERT: n 32 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5371 (t0) REVERT: o 36 ASN cc_start: 0.9112 (m-40) cc_final: 0.8629 (m110) REVERT: o 77 TYR cc_start: 0.8434 (t80) cc_final: 0.7924 (t80) REVERT: p 56 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6787 (mmm160) REVERT: q 5 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5946 (ttp-170) REVERT: r 56 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7580 (mtt90) REVERT: s 16 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7842 (pttt) REVERT: s 31 ARG cc_start: 0.7051 (ttp80) cc_final: 0.5727 (ttp-170) REVERT: s 43 MET cc_start: 0.7036 (ptp) cc_final: 0.6256 (ttm) REVERT: s 70 LEU cc_start: 0.8574 (mp) cc_final: 0.7958 (mp) REVERT: s 72 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7253 (mp0) REVERT: t 53 MET cc_start: 0.8352 (ppp) cc_final: 0.7727 (ppp) REVERT: u 12 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6405 (p0) REVERT: u 16 ARG cc_start: 0.7742 (ttp80) cc_final: 0.6885 (ptp90) REVERT: u 54 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7335 (ptt180) outliers start: 317 outliers final: 249 residues processed: 1371 average time/residue: 1.3971 time to fit residues: 3348.9948 Evaluate side-chains 1432 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1171 time to evaluate : 5.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 34 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 ASN Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 102 ASP Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 42 ASN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 71 VAL Chi-restraints excluded: chain y residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 741 optimal weight: 30.0000 chunk 574 optimal weight: 10.0000 chunk 855 optimal weight: 20.0000 chunk 567 optimal weight: 4.9990 chunk 1012 optimal weight: 0.0870 chunk 633 optimal weight: 0.9980 chunk 616 optimal weight: 7.9990 chunk 467 optimal weight: 40.0000 overall best weight: 3.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 11 ASN J 136 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN X 16 ASN c 138 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 21 HIS l 72 ASN m 11 HIS ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 159159 Z= 0.194 Angle : 0.678 31.509 237926 Z= 0.358 Chirality : 0.036 0.543 30321 Planarity : 0.006 0.125 12937 Dihedral : 24.690 179.320 79116 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.07 % Favored : 90.82 % Rotamer: Outliers : 4.95 % Allowed : 25.61 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.10), residues: 5999 helix: -0.15 (0.12), residues: 1966 sheet: -2.02 (0.15), residues: 986 loop : -2.39 (0.11), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP c 166 HIS 0.008 0.001 HIS 6 41 PHE 0.029 0.002 PHE i 19 TYR 0.034 0.002 TYR c 41 ARG 0.012 0.000 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1276 time to evaluate : 6.374 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: C 123 ILE cc_start: 0.8993 (mm) cc_final: 0.8565 (mm) REVERT: E 24 ASN cc_start: 0.8761 (t0) cc_final: 0.8502 (t0) REVERT: E 91 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7354 (t70) REVERT: G 123 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7763 (tm-30) REVERT: G 148 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: G 176 LYS cc_start: 0.7333 (mptt) cc_final: 0.6150 (tmtt) REVERT: H 35 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6918 (mttt) REVERT: H 55 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7592 (mm-30) REVERT: H 83 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7138 (tttm) REVERT: J 106 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8523 (tppp) REVERT: K 2 ILE cc_start: 0.9120 (mm) cc_final: 0.8650 (mm) REVERT: L 27 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8660 (pp) REVERT: L 93 ASN cc_start: 0.7593 (p0) cc_final: 0.7374 (p0) REVERT: M 110 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: P 26 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7297 (tm-30) REVERT: Q 96 ASP cc_start: 0.8410 (t0) cc_final: 0.7827 (m-30) REVERT: R 68 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7403 (mtp180) REVERT: R 83 TYR cc_start: 0.8308 (t80) cc_final: 0.8052 (t80) REVERT: T 12 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7580 (mmp80) REVERT: X 15 ASN cc_start: 0.8830 (m110) cc_final: 0.8501 (m110) REVERT: X 67 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8593 (tt) REVERT: X 77 TYR cc_start: 0.6915 (p90) cc_final: 0.6385 (p90) REVERT: Y 49 ASP cc_start: 0.7698 (t70) cc_final: 0.7362 (t0) REVERT: b 39 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6857 (tp) REVERT: b 62 ARG cc_start: 0.7352 (tpp80) cc_final: 0.5922 (mmm160) REVERT: b 77 GLU cc_start: 0.6642 (mp0) cc_final: 0.6383 (mp0) REVERT: b 88 GLN cc_start: 0.5697 (mp10) cc_final: 0.5185 (mp10) REVERT: c 7 ASN cc_start: 0.8194 (t0) cc_final: 0.7759 (m-40) REVERT: c 149 LYS cc_start: 0.6478 (tttt) cc_final: 0.5847 (tptp) REVERT: c 166 TRP cc_start: 0.8096 (p-90) cc_final: 0.7614 (p-90) REVERT: d 50 TYR cc_start: 0.7056 (t80) cc_final: 0.6686 (t80) REVERT: d 72 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7227 (mtp-110) REVERT: e 44 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7267 (ttt-90) REVERT: f 25 TYR cc_start: 0.7921 (m-80) cc_final: 0.7515 (m-80) REVERT: g 32 ASP cc_start: 0.8179 (t70) cc_final: 0.7798 (t0) REVERT: g 47 GLU cc_start: 0.7425 (tp30) cc_final: 0.6982 (pp20) REVERT: g 59 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6180 (pm20) REVERT: g 142 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6800 (tpt90) REVERT: h 59 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6706 (tm-30) REVERT: h 72 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7404 (tm-30) REVERT: h 90 GLU cc_start: 0.7214 (mp0) cc_final: 0.6897 (pm20) REVERT: h 123 GLU cc_start: 0.8243 (tt0) cc_final: 0.8029 (tt0) REVERT: i 102 PHE cc_start: 0.5313 (m-10) cc_final: 0.4884 (m-80) REVERT: j 47 GLU cc_start: 0.7812 (tp30) cc_final: 0.7308 (tm-30) REVERT: j 73 LEU cc_start: 0.6678 (tt) cc_final: 0.6322 (tp) REVERT: j 88 MET cc_start: 0.7146 (tmm) cc_final: 0.6647 (tmm) REVERT: k 52 ARG cc_start: 0.6571 (tpt170) cc_final: 0.6337 (tpt90) REVERT: l 8 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7485 (mtp-110) REVERT: l 39 THR cc_start: 0.8105 (t) cc_final: 0.7736 (m) REVERT: m 26 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8595 (tmtt) REVERT: m 68 LEU cc_start: 0.7872 (tp) cc_final: 0.7526 (tp) REVERT: m 80 MET cc_start: 0.8183 (mtt) cc_final: 0.7941 (mtt) REVERT: n 13 VAL cc_start: 0.7749 (m) cc_final: 0.7538 (t) REVERT: n 32 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5631 (t0) REVERT: n 86 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7621 (pp20) REVERT: o 36 ASN cc_start: 0.9070 (m-40) cc_final: 0.8571 (m110) REVERT: o 77 TYR cc_start: 0.8336 (t80) cc_final: 0.7948 (t80) REVERT: q 5 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5860 (ttp-170) REVERT: q 38 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8132 (mtmt) REVERT: s 16 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7770 (pttt) REVERT: s 31 ARG cc_start: 0.7015 (ttp80) cc_final: 0.5744 (ttp-170) REVERT: s 40 PHE cc_start: 0.7144 (m-10) cc_final: 0.6689 (m-10) REVERT: s 43 MET cc_start: 0.6818 (ptp) cc_final: 0.6454 (ptm) REVERT: t 53 MET cc_start: 0.8379 (ppp) cc_final: 0.8073 (ppp) REVERT: u 12 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5657 (p0) REVERT: u 16 ARG cc_start: 0.7744 (ttp80) cc_final: 0.6858 (ptp90) REVERT: u 54 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7276 (ptt180) outliers start: 235 outliers final: 178 residues processed: 1394 average time/residue: 1.3661 time to fit residues: 3308.1873 Evaluate side-chains 1389 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1200 time to evaluate : 6.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 34 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 19 PHE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 ASN Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 8 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 9.9990 chunk 404 optimal weight: 5.9990 chunk 604 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 643 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 500 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 795 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN H 11 ASN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN c 138 GLN ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN s 42 ASN ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 159159 Z= 0.321 Angle : 0.730 32.725 237926 Z= 0.381 Chirality : 0.040 0.549 30321 Planarity : 0.006 0.132 12937 Dihedral : 24.638 179.184 79114 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.24 % Favored : 88.65 % Rotamer: Outliers : 5.35 % Allowed : 25.78 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 5999 helix: -0.22 (0.12), residues: 1965 sheet: -2.00 (0.15), residues: 1013 loop : -2.39 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 166 HIS 0.007 0.001 HIS s 68 PHE 0.029 0.002 PHE p 38 TYR 0.032 0.002 TYR Q 31 ARG 0.013 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1206 time to evaluate : 6.398 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: 6 47 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7064 (pttm) REVERT: C 123 ILE cc_start: 0.9040 (mm) cc_final: 0.8598 (mm) REVERT: E 91 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7313 (t70) REVERT: G 123 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7804 (tm-30) REVERT: G 148 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7677 (ttt-90) REVERT: G 176 LYS cc_start: 0.7364 (mptt) cc_final: 0.6206 (tmtt) REVERT: H 35 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6952 (mttt) REVERT: J 106 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8540 (tppp) REVERT: L 27 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8683 (pp) REVERT: L 93 ASN cc_start: 0.7642 (p0) cc_final: 0.7420 (p0) REVERT: P 26 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7337 (tm-30) REVERT: Q 96 ASP cc_start: 0.8347 (t0) cc_final: 0.7784 (m-30) REVERT: R 68 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7468 (mtp180) REVERT: R 83 TYR cc_start: 0.8350 (t80) cc_final: 0.8085 (t80) REVERT: X 15 ASN cc_start: 0.8851 (m110) cc_final: 0.8551 (m110) REVERT: X 77 TYR cc_start: 0.6967 (p90) cc_final: 0.6464 (p90) REVERT: Y 19 LEU cc_start: 0.9003 (mm) cc_final: 0.8771 (mp) REVERT: b 39 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6977 (tp) REVERT: b 62 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6006 (mmm160) REVERT: b 88 GLN cc_start: 0.5639 (mp10) cc_final: 0.5091 (mp10) REVERT: c 7 ASN cc_start: 0.8267 (t0) cc_final: 0.7848 (m-40) REVERT: c 149 LYS cc_start: 0.6548 (tttt) cc_final: 0.5934 (tptp) REVERT: d 50 TYR cc_start: 0.7112 (t80) cc_final: 0.6732 (t80) REVERT: d 72 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7144 (mtp-110) REVERT: e 44 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7558 (ttt-90) REVERT: e 155 LYS cc_start: 0.6676 (ttpp) cc_final: 0.5883 (tttp) REVERT: f 21 MET cc_start: 0.6835 (mmt) cc_final: 0.6610 (mmt) REVERT: f 25 TYR cc_start: 0.7987 (m-80) cc_final: 0.7664 (m-80) REVERT: g 15 PRO cc_start: 0.6112 (Cg_exo) cc_final: 0.5746 (Cg_endo) REVERT: g 32 ASP cc_start: 0.8340 (t70) cc_final: 0.7951 (t0) REVERT: g 47 GLU cc_start: 0.7451 (tp30) cc_final: 0.6992 (pp20) REVERT: g 59 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5868 (pm20) REVERT: g 142 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6610 (mmm160) REVERT: h 72 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7464 (tm-30) REVERT: i 102 PHE cc_start: 0.5338 (m-10) cc_final: 0.4934 (m-80) REVERT: j 73 LEU cc_start: 0.6682 (tt) cc_final: 0.6351 (tp) REVERT: j 88 MET cc_start: 0.7099 (tmm) cc_final: 0.6572 (tmm) REVERT: k 52 ARG cc_start: 0.6617 (tpt170) cc_final: 0.6395 (tpt90) REVERT: l 8 ARG cc_start: 0.7767 (ttp-110) cc_final: 0.7516 (mtp-110) REVERT: l 39 THR cc_start: 0.8196 (t) cc_final: 0.7851 (m) REVERT: m 26 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8497 (tptp) REVERT: m 41 ASP cc_start: 0.6981 (p0) cc_final: 0.6043 (p0) REVERT: m 68 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7562 (tp) REVERT: m 80 MET cc_start: 0.8239 (mtt) cc_final: 0.8004 (mtt) REVERT: n 13 VAL cc_start: 0.7602 (m) cc_final: 0.7299 (t) REVERT: n 32 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5780 (t0) REVERT: o 36 ASN cc_start: 0.9087 (m-40) cc_final: 0.8598 (m110) REVERT: o 77 TYR cc_start: 0.8379 (t80) cc_final: 0.7854 (t80) REVERT: p 56 ARG cc_start: 0.7110 (mmm160) cc_final: 0.6757 (mmm160) REVERT: q 5 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5906 (ttp-170) REVERT: q 38 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8182 (mtmt) REVERT: s 16 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7781 (pttt) REVERT: s 31 ARG cc_start: 0.6927 (ttp80) cc_final: 0.5668 (ttp-170) REVERT: t 53 MET cc_start: 0.8436 (ppp) cc_final: 0.8102 (ppp) REVERT: u 12 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.5709 (p0) REVERT: u 16 ARG cc_start: 0.7670 (ttp80) cc_final: 0.6786 (ptp90) REVERT: u 54 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7350 (ptt180) outliers start: 254 outliers final: 219 residues processed: 1346 average time/residue: 1.2905 time to fit residues: 3008.2103 Evaluate side-chains 1405 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1177 time to evaluate : 8.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 34 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 ASN Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 119 LYS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 4.9990 chunk 969 optimal weight: 3.9990 chunk 884 optimal weight: 5.9990 chunk 943 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 410 optimal weight: 7.9990 chunk 740 optimal weight: 40.0000 chunk 289 optimal weight: 20.0000 chunk 852 optimal weight: 7.9990 chunk 891 optimal weight: 8.9990 chunk 939 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 159159 Z= 0.250 Angle : 0.697 31.911 237926 Z= 0.366 Chirality : 0.037 0.517 30321 Planarity : 0.006 0.128 12937 Dihedral : 24.629 179.782 79114 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.78 % Favored : 90.12 % Rotamer: Outliers : 5.16 % Allowed : 26.62 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 5999 helix: -0.15 (0.12), residues: 1960 sheet: -1.95 (0.15), residues: 1001 loop : -2.33 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 166 HIS 0.006 0.001 HIS 6 41 PHE 0.028 0.002 PHE n 20 TYR 0.034 0.002 TYR y 51 ARG 0.014 0.000 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1464 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1219 time to evaluate : 6.396 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: 6 47 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7043 (pttm) REVERT: C 123 ILE cc_start: 0.9018 (mm) cc_final: 0.8614 (mm) REVERT: C 179 GLU cc_start: 0.8160 (tt0) cc_final: 0.7764 (tt0) REVERT: E 24 ASN cc_start: 0.8810 (t0) cc_final: 0.8574 (t0) REVERT: E 91 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7349 (t70) REVERT: G 123 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7785 (tm-30) REVERT: G 148 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7639 (ttt-90) REVERT: G 176 LYS cc_start: 0.7336 (mptt) cc_final: 0.6143 (tmtt) REVERT: H 35 LYS cc_start: 0.7262 (mmtt) cc_final: 0.6942 (mttt) REVERT: J 106 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8534 (tppp) REVERT: L 27 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8653 (pp) REVERT: L 93 ASN cc_start: 0.7615 (p0) cc_final: 0.7392 (p0) REVERT: M 53 MET cc_start: 0.8199 (ttp) cc_final: 0.7957 (ttp) REVERT: M 110 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: P 26 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7329 (tm-30) REVERT: Q 96 ASP cc_start: 0.8365 (t0) cc_final: 0.7775 (m-30) REVERT: R 68 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7443 (mtp180) REVERT: R 83 TYR cc_start: 0.8319 (t80) cc_final: 0.8103 (t80) REVERT: R 95 ASP cc_start: 0.6905 (t0) cc_final: 0.6669 (t70) REVERT: T 12 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7576 (mmp80) REVERT: T 68 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8285 (ptmt) REVERT: T 78 SER cc_start: 0.8603 (p) cc_final: 0.8298 (p) REVERT: V 1 MET cc_start: 0.7530 (tpt) cc_final: 0.7273 (tpt) REVERT: X 15 ASN cc_start: 0.8848 (m110) cc_final: 0.8539 (m110) REVERT: X 67 LEU cc_start: 0.8376 (tt) cc_final: 0.8055 (mm) REVERT: X 77 TYR cc_start: 0.6982 (p90) cc_final: 0.6478 (p90) REVERT: Y 19 LEU cc_start: 0.8912 (mm) cc_final: 0.8634 (mp) REVERT: Y 49 ASP cc_start: 0.7739 (t70) cc_final: 0.7397 (t0) REVERT: b 26 MET cc_start: 0.8568 (mmm) cc_final: 0.8254 (mmt) REVERT: b 39 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6945 (tp) REVERT: b 62 ARG cc_start: 0.7356 (tpp80) cc_final: 0.5942 (mmm160) REVERT: b 77 GLU cc_start: 0.6631 (mp0) cc_final: 0.6397 (mp0) REVERT: b 88 GLN cc_start: 0.5736 (mp10) cc_final: 0.5213 (mp10) REVERT: c 7 ASN cc_start: 0.8284 (t0) cc_final: 0.7828 (m-40) REVERT: c 149 LYS cc_start: 0.6500 (tttt) cc_final: 0.5908 (tptp) REVERT: d 50 TYR cc_start: 0.7068 (t80) cc_final: 0.6690 (t80) REVERT: d 72 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7279 (mtp-110) REVERT: e 42 ASN cc_start: 0.8662 (t0) cc_final: 0.8350 (t0) REVERT: e 145 ASN cc_start: 0.8169 (m-40) cc_final: 0.7811 (m-40) REVERT: e 146 MET cc_start: 0.8441 (tpp) cc_final: 0.8052 (tpt) REVERT: f 25 TYR cc_start: 0.7872 (m-80) cc_final: 0.7662 (m-80) REVERT: f 35 LYS cc_start: 0.8341 (tttp) cc_final: 0.7731 (pttp) REVERT: f 39 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (tt) REVERT: g 32 ASP cc_start: 0.8171 (t70) cc_final: 0.7857 (t0) REVERT: g 47 GLU cc_start: 0.7435 (tp30) cc_final: 0.6989 (pp20) REVERT: g 59 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5858 (pm20) REVERT: g 100 MET cc_start: 0.7354 (mtt) cc_final: 0.7116 (mtp) REVERT: g 142 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6600 (mmm160) REVERT: h 4 ASP cc_start: 0.7282 (t0) cc_final: 0.6873 (m-30) REVERT: h 42 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7650 (tm-30) REVERT: h 72 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7404 (tm-30) REVERT: i 102 PHE cc_start: 0.5322 (m-10) cc_final: 0.4942 (m-80) REVERT: j 73 LEU cc_start: 0.6804 (tt) cc_final: 0.6435 (tp) REVERT: j 88 MET cc_start: 0.7125 (tmm) cc_final: 0.6597 (tmm) REVERT: l 8 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7463 (mtp-110) REVERT: l 39 THR cc_start: 0.8138 (t) cc_final: 0.7781 (m) REVERT: m 26 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8309 (tptt) REVERT: m 30 LYS cc_start: 0.8399 (pttt) cc_final: 0.7954 (mttt) REVERT: m 68 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7528 (tp) REVERT: m 80 MET cc_start: 0.8179 (mtt) cc_final: 0.7925 (mtt) REVERT: n 13 VAL cc_start: 0.7625 (m) cc_final: 0.7313 (t) REVERT: n 32 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5662 (t0) REVERT: o 36 ASN cc_start: 0.9072 (m-40) cc_final: 0.8592 (m110) REVERT: o 77 TYR cc_start: 0.8383 (t80) cc_final: 0.7986 (t80) REVERT: p 47 GLU cc_start: 0.3710 (OUTLIER) cc_final: 0.3056 (tm-30) REVERT: p 56 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6811 (mmm160) REVERT: q 5 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5914 (ttp-170) REVERT: q 38 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8100 (mtmt) REVERT: s 16 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7765 (pttt) REVERT: s 31 ARG cc_start: 0.6960 (ttp80) cc_final: 0.5727 (ttp-170) REVERT: t 53 MET cc_start: 0.8439 (ppp) cc_final: 0.8120 (ppp) REVERT: u 12 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.5670 (p0) REVERT: u 16 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6860 (ptp90) REVERT: u 54 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7349 (ptt180) outliers start: 245 outliers final: 214 residues processed: 1347 average time/residue: 1.3052 time to fit residues: 3051.7505 Evaluate side-chains 1416 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1190 time to evaluate : 6.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 34 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 19 PHE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 80 LEU Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 ASN Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 119 LYS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 73 PHE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 30.0000 chunk 997 optimal weight: 9.9990 chunk 608 optimal weight: 8.9990 chunk 473 optimal weight: 0.9990 chunk 693 optimal weight: 40.0000 chunk 1046 optimal weight: 3.9990 chunk 962 optimal weight: 7.9990 chunk 832 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 643 optimal weight: 9.9990 chunk 510 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN J 136 GLN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN d 197 HIS ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 159159 Z= 0.250 Angle : 0.694 31.040 237926 Z= 0.365 Chirality : 0.037 0.513 30321 Planarity : 0.006 0.129 12937 Dihedral : 24.594 179.858 79114 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.35 % Favored : 89.55 % Rotamer: Outliers : 5.03 % Allowed : 26.75 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 5999 helix: -0.14 (0.12), residues: 1962 sheet: -1.90 (0.15), residues: 1001 loop : -2.26 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 166 HIS 0.007 0.001 HIS e 82 PHE 0.028 0.002 PHE n 20 TYR 0.035 0.002 TYR e 49 ARG 0.013 0.000 ARG G 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11998 Ramachandran restraints generated. 5999 Oldfield, 0 Emsley, 5999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1207 time to evaluate : 6.478 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: 6 47 LYS cc_start: 0.7587 (mmmt) cc_final: 0.7009 (pttm) REVERT: C 123 ILE cc_start: 0.9038 (mm) cc_final: 0.8626 (mm) REVERT: C 179 GLU cc_start: 0.8137 (tt0) cc_final: 0.7725 (tt0) REVERT: C 202 ARG cc_start: 0.7779 (ptp-110) cc_final: 0.7491 (ptp90) REVERT: E 24 ASN cc_start: 0.8818 (t0) cc_final: 0.8571 (t0) REVERT: E 91 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7318 (t70) REVERT: G 87 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: G 123 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7789 (tm-30) REVERT: G 148 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7613 (ttt-90) REVERT: G 176 LYS cc_start: 0.7341 (mptt) cc_final: 0.6118 (tmtt) REVERT: H 35 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6867 (mttt) REVERT: J 106 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8533 (tppp) REVERT: L 27 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8657 (pp) REVERT: L 93 ASN cc_start: 0.7607 (p0) cc_final: 0.7381 (p0) REVERT: M 110 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: P 26 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7316 (tm-30) REVERT: Q 96 ASP cc_start: 0.8364 (t0) cc_final: 0.7763 (m-30) REVERT: R 68 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7504 (mtp180) REVERT: R 83 TYR cc_start: 0.8315 (t80) cc_final: 0.8097 (t80) REVERT: R 95 ASP cc_start: 0.6926 (t0) cc_final: 0.6683 (t70) REVERT: T 12 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7555 (mmp80) REVERT: T 68 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8308 (ttmt) REVERT: T 78 SER cc_start: 0.8566 (p) cc_final: 0.8277 (p) REVERT: V 1 MET cc_start: 0.7516 (tpt) cc_final: 0.7301 (tpt) REVERT: X 15 ASN cc_start: 0.8855 (m110) cc_final: 0.8544 (m110) REVERT: X 67 LEU cc_start: 0.8450 (tt) cc_final: 0.8110 (mm) REVERT: X 77 TYR cc_start: 0.6959 (p90) cc_final: 0.6402 (p90) REVERT: Y 19 LEU cc_start: 0.8809 (mm) cc_final: 0.8575 (mp) REVERT: b 26 MET cc_start: 0.8550 (mmm) cc_final: 0.8273 (mmt) REVERT: b 39 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7035 (tp) REVERT: b 62 ARG cc_start: 0.7362 (tpp80) cc_final: 0.5959 (mmm160) REVERT: b 77 GLU cc_start: 0.6604 (mp0) cc_final: 0.6369 (mp0) REVERT: b 88 GLN cc_start: 0.5749 (mp10) cc_final: 0.5229 (mp10) REVERT: c 7 ASN cc_start: 0.8257 (t0) cc_final: 0.7807 (m-40) REVERT: c 149 LYS cc_start: 0.6448 (tttt) cc_final: 0.5807 (tptp) REVERT: c 166 TRP cc_start: 0.8162 (p-90) cc_final: 0.7772 (p-90) REVERT: d 50 TYR cc_start: 0.7112 (t80) cc_final: 0.6729 (t80) REVERT: e 42 ASN cc_start: 0.8522 (t0) cc_final: 0.8228 (t0) REVERT: e 145 ASN cc_start: 0.8310 (m-40) cc_final: 0.7961 (m-40) REVERT: f 25 TYR cc_start: 0.7951 (m-80) cc_final: 0.7676 (m-80) REVERT: f 35 LYS cc_start: 0.8422 (tttp) cc_final: 0.7920 (pttp) REVERT: f 39 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8070 (tt) REVERT: g 32 ASP cc_start: 0.8106 (t70) cc_final: 0.7832 (t0) REVERT: g 47 GLU cc_start: 0.7432 (tp30) cc_final: 0.6991 (pp20) REVERT: g 59 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: g 100 MET cc_start: 0.7347 (mtt) cc_final: 0.7115 (mtp) REVERT: g 142 ARG cc_start: 0.7285 (mtm110) cc_final: 0.6601 (mmm160) REVERT: h 42 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7633 (tm-30) REVERT: h 72 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7363 (tm-30) REVERT: i 102 PHE cc_start: 0.5355 (m-10) cc_final: 0.4910 (m-80) REVERT: j 73 LEU cc_start: 0.6819 (tt) cc_final: 0.6470 (tp) REVERT: j 88 MET cc_start: 0.7116 (tmm) cc_final: 0.6596 (tmm) REVERT: l 39 THR cc_start: 0.8137 (t) cc_final: 0.7783 (m) REVERT: m 26 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8473 (tmtt) REVERT: m 41 ASP cc_start: 0.6945 (p0) cc_final: 0.6331 (p0) REVERT: m 68 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7561 (tp) REVERT: m 80 MET cc_start: 0.8186 (mtt) cc_final: 0.7934 (mtt) REVERT: n 13 VAL cc_start: 0.7619 (m) cc_final: 0.7306 (t) REVERT: n 32 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5678 (t0) REVERT: o 36 ASN cc_start: 0.9074 (m-40) cc_final: 0.8589 (m110) REVERT: o 77 TYR cc_start: 0.8389 (t80) cc_final: 0.7985 (t80) REVERT: p 47 GLU cc_start: 0.3447 (OUTLIER) cc_final: 0.2838 (tm-30) REVERT: p 56 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6867 (mmm160) REVERT: q 5 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5896 (ttp-170) REVERT: q 38 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8094 (mtmt) REVERT: s 16 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7758 (pttt) REVERT: s 31 ARG cc_start: 0.6980 (ttp80) cc_final: 0.5745 (ttp-170) REVERT: t 53 MET cc_start: 0.8459 (ppp) cc_final: 0.7736 (ppp) REVERT: u 12 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.5916 (p0) REVERT: u 16 ARG cc_start: 0.7741 (ttp80) cc_final: 0.6866 (ptp90) REVERT: u 23 GLU cc_start: 0.6368 (pt0) cc_final: 0.6131 (tt0) REVERT: u 54 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7388 (ptt180) outliers start: 239 outliers final: 210 residues processed: 1335 average time/residue: 1.2694 time to fit residues: 2946.8259 Evaluate side-chains 1408 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1186 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 34 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 51 VAL Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b residue 18 GLN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 202 PHE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 19 PHE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 99 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 ASN Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 119 LYS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 47 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 ILE Chi-restraints excluded: chain y residue 17 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 40.0000 chunk 887 optimal weight: 6.9990 chunk 255 optimal weight: 50.0000 chunk 768 optimal weight: 40.0000 chunk 122 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 856 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 3 GLN ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Q 58 GLN X 16 ASN c 138 GLN ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072943 restraints weight = 473765.957| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.38 r_work: 0.3152 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 159159 Z= 0.417 Angle : 0.802 34.238 237926 Z= 0.413 Chirality : 0.043 0.531 30321 Planarity : 0.007 0.136 12937 Dihedral : 24.647 179.661 79114 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.17 % Favored : 87.73 % Rotamer: Outliers : 5.41 % Allowed : 26.70 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 5999 helix: -0.41 (0.12), residues: 1970 sheet: -1.99 (0.15), residues: 996 loop : -2.41 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 166 HIS 0.007 0.001 HIS s 68 PHE 0.032 0.002 PHE n 20 TYR 0.036 0.003 TYR y 51 ARG 0.013 0.001 ARG G 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45123.05 seconds wall clock time: 787 minutes 36.37 seconds (47256.37 seconds total)