Starting phenix.real_space_refine on Sat Mar 23 16:25:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obr_12801/03_2024/7obr_12801_neut_updated.pdb" } resolution = 2.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 4017 5.49 5 Mg 97 5.21 5 S 291 5.16 5 C 76594 2.51 5 N 27478 2.21 5 O 38219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 189": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R ARG 173": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S ARG 139": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a ARG 105": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "d PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "l ARG 28": "NH1" <-> "NH2" Residue "m ARG 97": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "s GLU 88": "OE1" <-> "OE2" Residue "u GLU 4": "OE1" <-> "OE2" Residue "u ARG 36": "NH1" <-> "NH2" Residue "u ARG 48": "NH1" <-> "NH2" Residue "u GLU 91": "OE1" <-> "OE2" Residue "u ARG 114": "NH1" <-> "NH2" Residue "x GLU 82": "OE1" <-> "OE2" Residue "x GLU 198": "OE1" <-> "OE2" Residue "x GLU 334": "OE1" <-> "OE2" Residue "x ARG 371": "NH1" <-> "NH2" Residue "z ARG 581": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146701 Number of models: 1 Model: "" Number of chains: 60 Chain: "1" Number of atoms: 5341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 5341 Classifications: {'RNA': 249} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 124, 'rna3p_pyr': 101} Link IDs: {'rna2p': 24, 'rna3p': 224} Chain breaks: 3 Chain: "5" Number of atoms: 74854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3493, 74854 Classifications: {'RNA': 3493} Modifications used: {'5*END': 1, 'rna2p_pur': 328, 'rna2p_pyr': 216, 'rna3p_pur': 1576, 'rna3p_pyr': 1372} Link IDs: {'rna2p': 544, 'rna3p': 2948} Chain breaks: 15 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 844 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "s" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 502 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "t" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain breaks: 1 Chain: "u" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1626 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 2, 'TRANS': 191} Chain: "w" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 607 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "x" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3773 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 12, 'TRANS': 475} Chain: "z" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 339 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "5" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Unusual residues: {' MG': 97} Classifications: {'undetermined': 97} Link IDs: {None: 96} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0NW4 SG CYS g 46 60.533 87.863 110.757 1.00 17.37 S ATOM A0O3W SG CYS g 83 59.574 83.650 111.244 1.00 9.05 S ATOM A0O4G SG CYS g 86 58.499 85.860 111.007 1.00 11.50 S ATOM A0PU7 SG CYS j 19 109.510 109.222 85.962 1.00 10.87 S ATOM A0PUZ SG CYS j 22 112.944 110.865 85.903 1.00 10.87 S ATOM A0PXI SG CYS j 34 110.222 112.266 88.159 1.00 10.87 S ATOM A0PY1 SG CYS j 37 110.010 112.671 84.384 1.00 10.87 S ATOM A0R6J SG CYS m 96 157.530 162.240 177.531 1.00 10.65 S ATOM A0R79 SG CYS m 99 158.532 158.679 176.620 1.00 10.87 S ATOM A0R9R SG CYS m 110 161.165 161.051 177.828 1.00 10.87 S ATOM A0RAZ SG CYS m 115 159.692 161.570 174.418 1.00 10.87 S ATOM A0RMN SG CYS o 12 102.169 204.457 89.391 1.00 15.28 S ATOM A0RNB SG CYS o 15 100.824 207.443 87.546 1.00 23.01 S ATOM A0S0C SG CYS o 72 98.671 205.705 90.229 1.00 17.77 S ATOM A0S1D SG CYS o 77 99.338 204.092 86.820 1.00 27.22 S ATOM A0SG3 SG CYS p 39 55.935 97.070 124.701 1.00 8.02 S ATOM A0SGQ SG CYS p 42 55.562 93.531 126.155 1.00 9.09 S ATOM A0SK4 SG CYS p 57 58.823 94.688 124.430 1.00 10.87 S ATOM A0SKK SG CYS p 60 55.496 93.934 122.551 1.00 10.87 S Time building chain proxies: 50.97, per 1000 atoms: 0.35 Number of scatterers: 146701 At special positions: 0 Unit cell: (258.94, 276.06, 269.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 291 16.00 P 4017 15.00 Mg 97 11.99 O 38219 8.00 N 27478 7.00 C 76594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.20 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " Number of angles added : 24 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13966 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: 267 helices and 64 sheets defined 45.3% alpha, 12.6% beta 1251 base pairs and 2123 stacking pairs defined. Time for finding SS restraints: 77.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.759A pdb=" N ARG A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 13' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.529A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.032A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.628A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 173 through 178 Proline residue: A 178 - end of helix Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.978A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.877A pdb=" N CYS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.940A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 4.580A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.650A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.347A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Proline residue: C 31 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 31' Processing helix chain 'C' and resid 33 through 49 removed outlier: 4.003A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 133 removed outlier: 4.091A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.622A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.390A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.042A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.776A pdb=" N ARG C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 236 through 242 Proline residue: C 242 - end of helix Processing helix chain 'C' and resid 253 through 264 removed outlier: 3.553A pdb=" N LEU C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.925A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.670A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 4.409A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.953A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.292A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.824A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.519A pdb=" N GLY D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 6.575A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.546A pdb=" N ASN D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 230' Processing helix chain 'D' and resid 232 through 251 removed outlier: 4.984A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 272 through 294 removed outlier: 4.227A pdb=" N ARG D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.787A pdb=" N MET E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 5.894A pdb=" N VAL E 133 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.623A pdb=" N VAL E 190 " --> pdb=" O HIS E 186 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 191' Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.771A pdb=" N PHE E 213 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 214' Processing helix chain 'E' and resid 239 through 258 removed outlier: 4.018A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 262 through 270 removed outlier: 5.319A pdb=" N VAL E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 5.075A pdb=" N VAL E 283 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'F' and resid 26 through 81 removed outlier: 3.590A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 128 through 139 removed outlier: 3.587A pdb=" N VAL F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.159A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 202 through 211 removed outlier: 5.259A pdb=" N TRP F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.512A pdb=" N LEU F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.680A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 4.735A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.585A pdb=" N GLN G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 123 removed outlier: 3.598A pdb=" N LYS G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.586A pdb=" N LYS G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 178 removed outlier: 4.813A pdb=" N VAL G 167 " --> pdb=" O PRO G 163 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.907A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS G 195 " --> pdb=" O CYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 226 removed outlier: 4.992A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 262 removed outlier: 3.860A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.893A pdb=" N ALA H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.952A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.044A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.465A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.120A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 3.925A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.220A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 3.665A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS I 213 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 4.075A pdb=" N LEU J 33 " --> pdb=" O SER J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 95 through 100 removed outlier: 3.786A pdb=" N PHE J 99 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N SER J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 95 through 100' Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.831A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY J 116 " --> pdb=" O HIS J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 116' Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.501A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.161A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 4.042A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 3.837A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE L 94 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 3.636A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 removed outlier: 3.889A pdb=" N GLU L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 139 through 147' Processing helix chain 'L' and resid 170 through 177 removed outlier: 5.865A pdb=" N LYS L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 192 Processing helix chain 'L' and resid 193 through 211 Processing helix chain 'M' and resid 51 through 56 removed outlier: 4.007A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 6.492A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG M 74 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.519A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 Processing helix chain 'M' and resid 106 through 139 removed outlier: 3.701A pdb=" N ARG M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.132A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.616A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 4.038A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.602A pdb=" N GLY N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.069A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 147 through 153 removed outlier: 6.379A pdb=" N ILE N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR N 152 " --> pdb=" O THR N 148 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS N 153 " --> pdb=" O GLN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 153' Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.517A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.586A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.680A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 removed outlier: 3.532A pdb=" N ASN O 50 " --> pdb=" O ASN O 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.593A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.661A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.596A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 150 through 190 removed outlier: 5.396A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE O 189 " --> pdb=" O VAL O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 3.515A pdb=" N HIS O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.531A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY P 77 " --> pdb=" O ALA P 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 70 through 77' Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.547A pdb=" N ALA P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 54 removed outlier: 4.038A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.721A pdb=" N LEU Q 72 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.558A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 6.539A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.594A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN R 34 " --> pdb=" O ASN R 30 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.608A pdb=" N ILE R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.746A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.506A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 removed outlier: 3.507A pdb=" N SER S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 3.642A pdb=" N ILE S 124 " --> pdb=" O ARG S 120 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 120 through 125' Processing helix chain 'S' and resid 139 through 147 removed outlier: 4.421A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.550A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 11 through 16' Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.466A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 26 through 32' Processing helix chain 'T' and resid 92 through 97 removed outlier: 3.911A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 100 through 120 removed outlier: 4.218A pdb=" N SER T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 5.186A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU U 30 " --> pdb=" O THR U 26 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP U 31 " --> pdb=" O HIS U 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY U 32 " --> pdb=" O PRO U 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 25 through 32' Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 55 through 60 removed outlier: 5.199A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 55 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 4.240A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 3.540A pdb=" N ARG V 73 " --> pdb=" O LYS V 69 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 69 through 74' Processing helix chain 'V' and resid 122 through 130 Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 136 removed outlier: 3.626A pdb=" N ASN V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 removed outlier: 3.652A pdb=" N LYS W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 50 removed outlier: 3.858A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 78 removed outlier: 4.162A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 105 through 117 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 22 through 31 removed outlier: 3.543A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.029A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.583A pdb=" N ILE Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.586A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.828A pdb=" N VAL Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 104 removed outlier: 5.056A pdb=" N ARG Z 102 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP Z 103 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 124 removed outlier: 3.679A pdb=" N LYS Z 123 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 removed outlier: 4.123A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 132' Processing helix chain 'a' and resid 2 through 7 removed outlier: 3.749A pdb=" N ARG a 6 " --> pdb=" O PRO a 2 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2 through 7' Processing helix chain 'a' and resid 41 through 48 Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.047A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.977A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 91 removed outlier: 3.936A pdb=" N ALA a 90 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 removed outlier: 3.865A pdb=" N SER a 106 " --> pdb=" O ASP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.204A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY b 20 " --> pdb=" O TRP b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 54 removed outlier: 4.922A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLY b 53 " --> pdb=" O HIS b 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 76 Processing helix chain 'c' and resid 13 through 24 removed outlier: 4.310A pdb=" N ARG c 17 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 removed outlier: 3.543A pdb=" N GLY c 86 " --> pdb=" O GLY c 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 34 removed outlier: 3.782A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS d 34 " --> pdb=" O HIS d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 57 removed outlier: 4.051A pdb=" N ARG d 44 " --> pdb=" O LYS d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.617A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 29' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 81 through 90 removed outlier: 3.787A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.638A pdb=" N LYS e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 43 removed outlier: 4.227A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE f 41 " --> pdb=" O ASP f 37 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR f 42 " --> pdb=" O GLU f 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.586A pdb=" N LEU g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER g 68 " --> pdb=" O LEU g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.508A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.610A pdb=" N GLY h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 40 through 74 removed outlier: 3.613A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 95 removed outlier: 3.554A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU h 95 " --> pdb=" O MET h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 103 removed outlier: 6.673A pdb=" N GLU h 100 " --> pdb=" O ASN h 96 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS h 103 " --> pdb=" O GLU h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.280A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.547A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 103 removed outlier: 4.341A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.773A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.612A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.529A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.684A pdb=" N ARG k 17 " --> pdb=" O LEU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 removed outlier: 4.171A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 4.222A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.464A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.924A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.832A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 47 removed outlier: 5.476A pdb=" N GLY o 47 " --> pdb=" O ARG o 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 4.053A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 19 through 25 removed outlier: 4.368A pdb=" N LEU q 23 " --> pdb=" O TYR q 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN q 24 " --> pdb=" O PRO q 20 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN q 25 " --> pdb=" O ALA q 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 19 through 25' Processing helix chain 'q' and resid 45 through 57 removed outlier: 3.772A pdb=" N ILE q 49 " --> pdb=" O THR q 45 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA q 55 " --> pdb=" O ASP q 51 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL q 56 " --> pdb=" O VAL q 52 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY q 57 " --> pdb=" O CYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 80 removed outlier: 3.852A pdb=" N ARG q 79 " --> pdb=" O ASP q 75 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY q 80 " --> pdb=" O VAL q 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 75 through 80' Processing helix chain 'q' and resid 100 through 117 removed outlier: 3.670A pdb=" N VAL q 104 " --> pdb=" O SER q 100 " (cutoff:3.500A) Proline residue: q 113 - end of helix removed outlier: 4.283A pdb=" N LYS q 116 " --> pdb=" O ILE q 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 13 removed outlier: 5.355A pdb=" N ASN r 12 " --> pdb=" O MET r 8 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS r 13 " --> pdb=" O VAL r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 72 through 77 removed outlier: 4.542A pdb=" N TYR r 77 " --> pdb=" O PRO r 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 98 removed outlier: 6.061A pdb=" N THR r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU r 90 " --> pdb=" O ALA r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 122 removed outlier: 4.322A pdb=" N ARG r 107 " --> pdb=" O HIS r 103 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) Processing helix chain 's' and resid 24 through 44 Processing helix chain 's' and resid 58 through 74 removed outlier: 5.056A pdb=" N SER s 62 " --> pdb=" O GLN s 58 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 21 removed outlier: 3.731A pdb=" N LEU t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR t 11 " --> pdb=" O GLU t 7 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG t 21 " --> pdb=" O PHE t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 91 removed outlier: 3.764A pdb=" N MET t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA t 82 " --> pdb=" O LYS t 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET t 91 " --> pdb=" O LEU t 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 17 removed outlier: 4.110A pdb=" N GLN u 15 " --> pdb=" O GLU u 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS u 16 " --> pdb=" O SER u 12 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY u 17 " --> pdb=" O GLN u 13 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 42 removed outlier: 4.130A pdb=" N TYR u 26 " --> pdb=" O ASP u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 62 removed outlier: 3.751A pdb=" N LEU u 61 " --> pdb=" O THR u 57 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR u 62 " --> pdb=" O GLU u 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 57 through 62' Processing helix chain 'u' and resid 65 through 89 removed outlier: 3.909A pdb=" N LEU u 69 " --> pdb=" O ARG u 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL u 70 " --> pdb=" O TYR u 66 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN u 89 " --> pdb=" O LYS u 85 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 118 removed outlier: 4.207A pdb=" N HIS u 97 " --> pdb=" O ARG u 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS u 104 " --> pdb=" O SER u 100 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS u 116 " --> pdb=" O LEU u 112 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU u 117 " --> pdb=" O GLU u 113 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER u 118 " --> pdb=" O ARG u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 145 removed outlier: 3.706A pdb=" N LYS u 126 " --> pdb=" O ASP u 122 " (cutoff:3.500A) Processing helix chain 'u' and resid 146 through 169 removed outlier: 3.705A pdb=" N ALA u 150 " --> pdb=" O GLU u 146 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N THR u 169 " --> pdb=" O ALA u 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 194 removed outlier: 3.683A pdb=" N VAL u 174 " --> pdb=" O GLU u 170 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU u 175 " --> pdb=" O GLU u 171 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR u 176 " --> pdb=" O GLN u 172 " (cutoff:3.500A) Proline residue: u 185 - end of helix removed outlier: 3.504A pdb=" N ILE u 194 " --> pdb=" O CYS u 190 " (cutoff:3.500A) Processing helix chain 'w' and resid 7 through 22 removed outlier: 6.673A pdb=" N SER w 11 " --> pdb=" O TRP w 7 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG w 12 " --> pdb=" O GLU w 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP w 21 " --> pdb=" O LEU w 17 " (cutoff:3.500A) Proline residue: w 22 - end of helix Processing helix chain 'w' and resid 55 through 75 removed outlier: 4.227A pdb=" N VAL w 59 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS w 61 " --> pdb=" O GLN w 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 3 through 19 removed outlier: 6.458A pdb=" N GLY x 7 " --> pdb=" O LEU x 3 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG x 8 " --> pdb=" O ALA x 4 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN x 19 " --> pdb=" O ARG x 15 " (cutoff:3.500A) Processing helix chain 'x' and resid 24 through 43 removed outlier: 3.892A pdb=" N LEU x 28 " --> pdb=" O ASN x 24 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN x 29 " --> pdb=" O GLU x 25 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU x 34 " --> pdb=" O ALA x 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU x 39 " --> pdb=" O VAL x 35 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP x 43 " --> pdb=" O LEU x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 45 through 61 removed outlier: 3.551A pdb=" N GLU x 54 " --> pdb=" O LYS x 50 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP x 61 " --> pdb=" O LYS x 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 88 removed outlier: 3.709A pdb=" N ALA x 78 " --> pdb=" O MET x 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL x 79 " --> pdb=" O ILE x 75 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 129 removed outlier: 3.593A pdb=" N SER x 119 " --> pdb=" O THR x 115 " (cutoff:3.500A) Processing helix chain 'x' and resid 143 through 156 Processing helix chain 'x' and resid 167 through 183 removed outlier: 3.580A pdb=" N ILE x 171 " --> pdb=" O ASP x 167 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN x 181 " --> pdb=" O GLU x 177 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU x 182 " --> pdb=" O LYS x 178 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN x 183 " --> pdb=" O PHE x 179 " (cutoff:3.500A) Processing helix chain 'x' and resid 198 through 213 removed outlier: 3.554A pdb=" N LEU x 206 " --> pdb=" O PHE x 202 " (cutoff:3.500A) Processing helix chain 'x' and resid 228 through 240 removed outlier: 3.703A pdb=" N GLN x 232 " --> pdb=" O ALA x 228 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS x 239 " --> pdb=" O ALA x 235 " (cutoff:3.500A) Processing helix chain 'x' and resid 256 through 267 removed outlier: 4.592A pdb=" N LEU x 260 " --> pdb=" O GLY x 256 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER x 261 " --> pdb=" O GLY x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 286 through 296 removed outlier: 3.511A pdb=" N LEU x 294 " --> pdb=" O PHE x 290 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY x 296 " --> pdb=" O SER x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 299 through 311 removed outlier: 4.531A pdb=" N LEU x 303 " --> pdb=" O ASP x 299 " (cutoff:3.500A) Processing helix chain 'x' and resid 314 through 325 removed outlier: 5.365A pdb=" N LEU x 318 " --> pdb=" O ASP x 314 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE x 319 " --> pdb=" O ASN x 315 " (cutoff:3.500A) Processing helix chain 'x' and resid 328 through 343 removed outlier: 4.071A pdb=" N GLY x 343 " --> pdb=" O ILE x 339 " (cutoff:3.500A) Processing helix chain 'x' and resid 344 through 353 removed outlier: 3.755A pdb=" N ILE x 348 " --> pdb=" O PRO x 344 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU x 349 " --> pdb=" O PHE x 345 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE x 352 " --> pdb=" O ILE x 348 " (cutoff:3.500A) Proline residue: x 353 - end of helix Processing helix chain 'x' and resid 363 through 383 removed outlier: 5.089A pdb=" N GLU x 367 " --> pdb=" O GLY x 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA x 370 " --> pdb=" O GLN x 366 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS x 374 " --> pdb=" O ALA x 370 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU x 375 " --> pdb=" O ARG x 371 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET x 376 " --> pdb=" O LEU x 372 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR x 377 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER x 381 " --> pdb=" O THR x 377 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET x 382 " --> pdb=" O ILE x 378 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN x 383 " --> pdb=" O MET x 379 " (cutoff:3.500A) Processing helix chain 'x' and resid 384 through 389 Processing helix chain 'x' and resid 391 through 400 removed outlier: 3.834A pdb=" N VAL x 395 " --> pdb=" O ASP x 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS x 398 " --> pdb=" O LYS x 394 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN x 399 " --> pdb=" O VAL x 395 " (cutoff:3.500A) Proline residue: x 400 - end of helix Processing helix chain 'x' and resid 401 through 411 removed outlier: 3.592A pdb=" N GLY x 409 " --> pdb=" O ARG x 405 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY x 411 " --> pdb=" O ALA x 407 " (cutoff:3.500A) Processing helix chain 'x' and resid 413 through 438 removed outlier: 4.060A pdb=" N GLN x 418 " --> pdb=" O THR x 414 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS x 438 " --> pdb=" O MET x 434 " (cutoff:3.500A) Processing helix chain 'x' and resid 451 through 467 removed outlier: 3.956A pdb=" N MET x 465 " --> pdb=" O GLN x 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET x 466 " --> pdb=" O MET x 462 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP x 467 " --> pdb=" O ALA x 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 468 through 475 removed outlier: 6.494A pdb=" N HIS x 472 " --> pdb=" O PRO x 468 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS x 473 " --> pdb=" O ARG x 469 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY x 475 " --> pdb=" O LEU x 471 " (cutoff:3.500A) Processing helix chain 'x' and resid 476 through 490 Processing helix chain 'x' and resid 356 through 361 removed outlier: 4.565A pdb=" N PHE x 359 " --> pdb=" O GLY x 356 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET x 360 " --> pdb=" O THR x 357 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER x 361 " --> pdb=" O ASP x 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 356 through 361' Processing helix chain 'z' and resid 561 through 569 removed outlier: 3.525A pdb=" N ASN z 565 " --> pdb=" O LYS z 561 " (cutoff:3.500A) Proline residue: z 568 - end of helix Processing helix chain 'z' and resid 593 through 599 removed outlier: 4.697A pdb=" N ILE z 598 " --> pdb=" O LYS z 594 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY z 599 " --> pdb=" O LYS z 595 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.845A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.778A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.806A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.734A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.748A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 286 through 290 removed outlier: 3.693A pdb=" N LYS B 286 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 330 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 76 through 80 Processing sheet with id= 9, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'C' and resid 226 through 232 removed outlier: 5.966A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 12, first strand: chain 'E' and resid 144 through 149 removed outlier: 4.373A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 142 through 146 removed outlier: 5.807A pdb=" N LYS F 90 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE F 120 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 161 through 164 Processing sheet with id= 15, first strand: chain 'G' and resid 179 through 184 removed outlier: 3.687A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 5 through 12 removed outlier: 6.094A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 18, first strand: chain 'H' and resid 102 through 106 removed outlier: 6.606A pdb=" N LEU H 111 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET H 128 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.229A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER H 94 " --> pdb=" O ASP H 142 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 88 through 91 Processing sheet with id= 21, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.071A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG I 162 " --> pdb=" O ASP I 55 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.643A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 189 through 192 removed outlier: 6.015A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.584A pdb=" N LYS J 19 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN J 23 " --> pdb=" O ASP J 129 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 48 through 52 Processing sheet with id= 26, first strand: chain 'M' and resid 11 through 16 removed outlier: 4.145A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.553A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL M 38 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG M 47 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.055A pdb=" N ALA N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.691A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 31, first strand: chain 'P' and resid 13 through 20 removed outlier: 7.278A pdb=" N LYS P 13 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 57 through 60 removed outlier: 3.705A pdb=" N PHE P 60 " --> pdb=" O GLN P 80 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'P' and resid 124 through 131 removed outlier: 4.002A pdb=" N MET P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 35, first strand: chain 'S' and resid 27 through 33 removed outlier: 6.457A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 92 through 99 removed outlier: 3.664A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.745A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 39 through 43 removed outlier: 3.962A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 61 through 65 removed outlier: 3.550A pdb=" N THR U 71 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU U 112 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE U 115 " --> pdb=" O TRP U 99 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TRP U 99 " --> pdb=" O PHE U 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 35 through 40 removed outlier: 5.864A pdb=" N LYS V 35 " --> pdb=" O CYS V 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN V 101 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= 42, first strand: chain 'V' and resid 87 through 90 removed outlier: 4.160A pdb=" N VAL V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 18 through 23 removed outlier: 3.863A pdb=" N LYS W 27 " --> pdb=" O ARG W 23 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 94 through 100 removed outlier: 6.807A pdb=" N ASN X 94 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU X 133 " --> pdb=" O ARG X 129 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS X 123 " --> pdb=" O ARG X 139 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Y' and resid 53 through 56 removed outlier: 5.358A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Y' and resid 71 through 75 removed outlier: 3.660A pdb=" N GLN Y 72 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.270A pdb=" N VAL Y 85 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Z' and resid 10 through 14 removed outlier: 4.311A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 27 through 30 removed outlier: 6.334A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.585A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU c 45 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.859A pdb=" N TYR d 103 " --> pdb=" O LYS d 91 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR d 22 " --> pdb=" O VAL d 122 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL d 120 " --> pdb=" O GLU d 24 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 53, first strand: chain 'f' and resid 8 through 12 removed outlier: 6.007A pdb=" N LYS f 8 " --> pdb=" O GLU f 31 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N MET f 83 " --> pdb=" O ALA f 77 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA f 77 " --> pdb=" O MET f 83 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 6 through 11 removed outlier: 4.452A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'g' and resid 20 through 24 Processing sheet with id= 56, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.816A pdb=" N ARG k 3 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS k 67 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE k 25 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'm' and resid 100 through 103 removed outlier: 6.165A pdb=" N LYS m 93 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'o' and resid 7 through 10 removed outlier: 5.599A pdb=" N VAL o 67 " --> pdb=" O TYR o 26 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.718A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY p 58 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 15 through 18 removed outlier: 3.504A pdb=" N ARG q 83 " --> pdb=" O PHE q 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE q 61 " --> pdb=" O ARG q 83 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN q 59 " --> pdb=" O GLN q 85 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 48 through 53 removed outlier: 5.303A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 't' and resid 27 through 32 Processing sheet with id= 63, first strand: chain 'w' and resid 26 through 33 Processing sheet with id= 64, first strand: chain 'x' and resid 158 through 161 removed outlier: 3.598A pdb=" N ILE x 188 " --> pdb=" O CYS x 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER x 192 " --> pdb=" O ALA x 137 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR x 191 " --> pdb=" O PHE x 106 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY x 108 " --> pdb=" O THR x 191 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER x 244 " --> pdb=" O ILE x 217 " (cutoff:3.500A) 2354 hydrogen bonds defined for protein. 6978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3275 hydrogen bonds 5616 hydrogen bond angles 0 basepair planarities 1251 basepair parallelities 2123 stacking parallelities Total time for adding SS restraints: 332.03 Time building geometry restraints manager: 58.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 25053 1.33 - 1.45: 60256 1.45 - 1.57: 64085 1.57 - 1.69: 8014 1.69 - 1.81: 471 Bond restraints: 157879 Sorted by residual: bond pdb=" C3' A 55061 " pdb=" O3' A 55061 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.63e+00 bond pdb=" C GLY s 40 " pdb=" O GLY s 40 " ideal model delta sigma weight residual 1.234 1.215 0.018 1.21e-02 6.83e+03 2.24e+00 bond pdb=" N GLY s 40 " pdb=" CA GLY s 40 " ideal model delta sigma weight residual 1.454 1.436 0.018 1.24e-02 6.50e+03 2.11e+00 bond pdb=" C LEU s 36 " pdb=" O LEU s 36 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.10e+00 bond pdb=" CA GLY s 40 " pdb=" C GLY s 40 " ideal model delta sigma weight residual 1.516 1.501 0.015 1.09e-02 8.42e+03 1.93e+00 ... (remaining 157874 not shown) Histogram of bond angle deviations from ideal: 99.85 - 107.12: 25165 107.12 - 114.40: 98909 114.40 - 121.67: 72586 121.67 - 128.95: 32265 128.95 - 136.22: 3618 Bond angle restraints: 232543 Sorted by residual: angle pdb=" N PRO s 60 " pdb=" CA PRO s 60 " pdb=" CB PRO s 60 " ideal model delta sigma weight residual 103.51 110.36 -6.85 9.60e-01 1.09e+00 5.09e+01 angle pdb=" C3' A 55061 " pdb=" O3' A 55061 " pdb=" P G 55062 " ideal model delta sigma weight residual 120.20 128.18 -7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C VAL s 30 " pdb=" CA VAL s 30 " pdb=" CB VAL s 30 " ideal model delta sigma weight residual 112.14 105.22 6.92 1.35e+00 5.49e-01 2.63e+01 angle pdb=" O3' A 55061 " pdb=" C3' A 55061 " pdb=" C2' A 55061 " ideal model delta sigma weight residual 109.50 116.19 -6.69 1.50e+00 4.44e-01 1.99e+01 angle pdb=" C3' G 53904 " pdb=" O3' G 53904 " pdb=" P A 53905 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 232538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 90702 36.00 - 72.00: 9947 72.00 - 108.00: 1365 108.00 - 144.00: 44 144.00 - 180.00: 97 Dihedral angle restraints: 102155 sinusoidal: 80498 harmonic: 21657 Sorted by residual: dihedral pdb=" C4' C 5 170 " pdb=" C3' C 5 170 " pdb=" C2' C 5 170 " pdb=" C1' C 5 170 " ideal model delta sinusoidal sigma weight residual -35.00 33.62 -68.62 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' C 5 170 " pdb=" C4' C 5 170 " pdb=" C3' C 5 170 " pdb=" O3' C 5 170 " ideal model delta sinusoidal sigma weight residual 147.00 78.96 68.04 1 8.00e+00 1.56e-02 9.39e+01 dihedral pdb=" O4' U 54758 " pdb=" C1' U 54758 " pdb=" N1 U 54758 " pdb=" C2 U 54758 " ideal model delta sinusoidal sigma weight residual -160.00 19.18 -179.18 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 102152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 27748 0.076 - 0.152: 1125 0.152 - 0.229: 59 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 28938 Sorted by residual: chirality pdb=" C3' C 5 170 " pdb=" C4' C 5 170 " pdb=" O3' C 5 170 " pdb=" C2' C 5 170 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3' G 53904 " pdb=" C4' G 53904 " pdb=" O3' G 53904 " pdb=" C2' G 53904 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO s 60 " pdb=" N PRO s 60 " pdb=" C PRO s 60 " pdb=" CB PRO s 60 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 28935 not shown) Planarity restraints: 14466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO f 107 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR s 41 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C THR s 41 " -0.050 2.00e-02 2.50e+03 pdb=" O THR s 41 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL s 42 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 54510 " 0.037 2.00e-02 2.50e+03 1.68e-02 7.79e+00 pdb=" N9 A 54510 " -0.040 2.00e-02 2.50e+03 pdb=" C8 A 54510 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 54510 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 54510 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 54510 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A 54510 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A 54510 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 54510 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 54510 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A 54510 " -0.005 2.00e-02 2.50e+03 ... (remaining 14463 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 617 2.45 - 3.06: 85068 3.06 - 3.67: 263606 3.67 - 4.29: 397201 4.29 - 4.90: 559079 Nonbonded interactions: 1305571 Sorted by model distance: nonbonded pdb=" NZ LYS x 9 " pdb=" CB ALA x 38 " model vdw 1.835 3.540 nonbonded pdb=" NZ LYS x 9 " pdb=" CA ALA x 38 " model vdw 1.931 3.550 nonbonded pdb=" O6 G 51321 " pdb="MG MG 55156 " model vdw 1.951 2.170 nonbonded pdb=" OP1 C 5 41 " pdb="MG MG 55141 " model vdw 1.979 2.170 nonbonded pdb=" OP1 A 54394 " pdb="MG MG 55156 " model vdw 1.983 2.170 ... (remaining 1305566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.57 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 21.260 Check model and map are aligned: 1.420 Set scattering table: 0.890 Process input model: 637.930 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 681.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.002 0.038 157879 Z= 0.107 Angle : 0.494 10.915 232543 Z= 0.273 Chirality : 0.031 0.381 28938 Planarity : 0.003 0.083 14466 Dihedral : 23.164 179.997 88189 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 2.55 % Allowed : 5.16 % Favored : 92.29 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7380 helix: 1.88 (0.10), residues: 2664 sheet: 0.35 (0.17), residues: 965 loop : -0.71 (0.10), residues: 3751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.004 0.001 HIS a 40 PHE 0.008 0.001 PHE M 64 TYR 0.012 0.001 TYR P 139 ARG 0.004 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1904 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1740 time to evaluate : 7.247 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: C 65 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 236 MET cc_start: 0.6688 (mmm) cc_final: 0.6467 (mmp) REVERT: E 115 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: E 141 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7121 (p) REVERT: M 17 PHE cc_start: 0.8356 (p90) cc_final: 0.8008 (p90) REVERT: N 103 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8168 (mt-10) REVERT: N 104 GLU cc_start: 0.7657 (tt0) cc_final: 0.7369 (tt0) REVERT: P 20 SER cc_start: 0.8305 (m) cc_final: 0.8094 (t) REVERT: P 130 TYR cc_start: 0.8508 (m-80) cc_final: 0.8097 (m-80) REVERT: R 66 ASN cc_start: 0.8802 (m-40) cc_final: 0.8600 (m-40) REVERT: R 144 LYS cc_start: 0.7478 (tppt) cc_final: 0.7082 (tppt) REVERT: S 93 MET cc_start: 0.8338 (mtt) cc_final: 0.8107 (mtt) REVERT: S 127 MET cc_start: 0.7871 (mtm) cc_final: 0.7585 (mtm) REVERT: T 146 LYS cc_start: 0.6359 (mtmm) cc_final: 0.6112 (mttt) REVERT: a 135 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6998 (mt-10) REVERT: c 93 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8291 (p) REVERT: g 5 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7861 (pp) REVERT: p 33 GLN cc_start: 0.8521 (tt0) cc_final: 0.8087 (tt0) REVERT: s 48 ILE cc_start: 0.6918 (pt) cc_final: 0.6711 (pt) REVERT: u 36 ARG cc_start: 0.3554 (tpt170) cc_final: 0.3205 (mtp85) REVERT: u 64 ASN cc_start: 0.3198 (OUTLIER) cc_final: 0.2535 (m110) REVERT: x 63 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4787 (pt0) outliers start: 164 outliers final: 42 residues processed: 1851 average time/residue: 2.3883 time to fit residues: 6176.2311 Evaluate side-chains 1089 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1041 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 111 MET Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain x residue 10 ILE Chi-restraints excluded: chain x residue 17 LEU Chi-restraints excluded: chain x residue 23 ILE Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 63 GLU Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 103 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 950 optimal weight: 0.9980 chunk 853 optimal weight: 9.9990 chunk 473 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 575 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 882 optimal weight: 0.8980 chunk 341 optimal weight: 10.0000 chunk 536 optimal weight: 6.9990 chunk 656 optimal weight: 0.9990 chunk 1022 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 179 HIS ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 281 ASN C 38 ASN C 119 GLN C 299 GLN D 39 GLN D 63 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 39 HIS E 124 HIS F 41 GLN F 118 GLN F 165 ASN G 82 GLN G 112 GLN G 206 GLN H 8 GLN H 79 ASN H 156 ASN I 202 ASN J 42 GLN J 98 ASN L 40 GLN L 104 ASN L 113 ASN N 8 GLN P 25 HIS P 75 GLN P 118 GLN Q 8 ASN Q 160 HIS Q 188 ASN R 39 GLN R 86 ASN S 50 GLN U 27 HIS U 95 ASN V 36 ASN X 93 ASN X 125 ASN Y 43 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 ASN Z 132 GLN a 66 ASN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN f 80 ASN i 15 HIS l 19 GLN l 33 ASN m 84 GLN m 90 ASN q 88 GLN r 6 GLN r 30 ASN r 83 ASN r 100 ASN r 103 HIS s 50 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 47 ASN u 83 GLN x 24 ASN ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 454 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 157879 Z= 0.241 Angle : 0.634 10.662 232543 Z= 0.322 Chirality : 0.037 0.364 28938 Planarity : 0.005 0.083 14466 Dihedral : 24.600 179.869 72312 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 5.56 % Allowed : 15.05 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 7380 helix: 1.62 (0.10), residues: 2710 sheet: 0.11 (0.16), residues: 991 loop : -0.85 (0.10), residues: 3679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 211 HIS 0.009 0.001 HIS B 55 PHE 0.022 0.002 PHE d 52 TYR 0.025 0.002 TYR P 139 ARG 0.009 0.001 ARG P 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1082 time to evaluate : 7.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7060 (ptm160) REVERT: A 74 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: C 65 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 325 MET cc_start: 0.8781 (tpp) cc_final: 0.8391 (tpt) REVERT: E 141 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7393 (p) REVERT: E 228 ILE cc_start: -0.0578 (OUTLIER) cc_final: -0.0779 (mt) REVERT: E 241 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5778 (tt0) REVERT: F 202 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6528 (mpt-90) REVERT: H 128 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6515 (mmm) REVERT: I 56 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: I 123 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6730 (tp-100) REVERT: I 210 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7463 (mtt180) REVERT: J 83 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (tm) REVERT: M 17 PHE cc_start: 0.8519 (p90) cc_final: 0.8304 (p90) REVERT: N 104 GLU cc_start: 0.7766 (tt0) cc_final: 0.7506 (tt0) REVERT: O 113 ASP cc_start: 0.8236 (p0) cc_final: 0.7895 (p0) REVERT: O 162 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6497 (mt-10) REVERT: O 196 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8112 (mp) REVERT: R 98 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7729 (ttt180) REVERT: S 93 MET cc_start: 0.8559 (mtt) cc_final: 0.8241 (mtt) REVERT: S 99 ASP cc_start: 0.8159 (t0) cc_final: 0.7765 (t0) REVERT: S 108 GLN cc_start: 0.8520 (mt0) cc_final: 0.8297 (mt0) REVERT: T 70 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.6152 (p90) REVERT: T 146 LYS cc_start: 0.6812 (mtmm) cc_final: 0.6232 (mttt) REVERT: V 73 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7955 (mtm180) REVERT: X 62 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7659 (mmp-170) REVERT: Z 21 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7399 (mpp-170) REVERT: Z 48 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7571 (ptt-90) REVERT: a 135 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7087 (mt-10) REVERT: d 64 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8914 (mm) REVERT: e 76 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8085 (ttmt) REVERT: g 32 TYR cc_start: 0.8990 (m-10) cc_final: 0.8735 (m-10) REVERT: i 56 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7654 (ttt90) REVERT: o 82 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7704 (mmp) REVERT: t 91 MET cc_start: 0.2139 (mtm) cc_final: 0.1902 (mmt) REVERT: u 64 ASN cc_start: 0.3223 (OUTLIER) cc_final: 0.2559 (m110) REVERT: u 106 VAL cc_start: 0.1964 (OUTLIER) cc_final: 0.1395 (t) REVERT: x 63 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4727 (pt0) REVERT: x 157 ILE cc_start: 0.3864 (OUTLIER) cc_final: 0.3275 (tp) REVERT: x 477 MET cc_start: 0.5859 (mmp) cc_final: 0.4321 (pmm) outliers start: 357 outliers final: 144 residues processed: 1295 average time/residue: 2.2244 time to fit residues: 4133.1328 Evaluate side-chains 1150 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 979 time to evaluate : 6.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 118 MET Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 135 ASN Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 62 ARG Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 76 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain u residue 50 LYS Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain x residue 23 ILE Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 63 GLU Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 337 GLN Chi-restraints excluded: chain x residue 340 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 568 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 851 optimal weight: 10.0000 chunk 696 optimal weight: 0.9980 chunk 282 optimal weight: 40.0000 chunk 1024 optimal weight: 7.9990 chunk 1106 optimal weight: 20.0000 chunk 912 optimal weight: 5.9990 chunk 1015 optimal weight: 7.9990 chunk 349 optimal weight: 10.0000 chunk 821 optimal weight: 0.4980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS F 118 GLN F 165 ASN G 206 GLN H 116 ASN L 104 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN Q 160 HIS ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS U 95 ASN ** V 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN X 107 HIS X 125 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN a 62 HIS a 67 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 7 HIS d 18 ASN d 116 ASN h 20 GLN l 19 GLN m 84 GLN m 120 ASN r 23 GLN r 30 ASN r 83 ASN ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 34 GLN x 19 ASN x 77 HIS ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 423 GLN x 452 GLN x 481 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 157879 Z= 0.233 Angle : 0.615 11.085 232543 Z= 0.314 Chirality : 0.037 0.348 28938 Planarity : 0.005 0.109 14466 Dihedral : 24.612 179.924 72293 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 6.23 % Allowed : 16.28 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 7380 helix: 1.59 (0.10), residues: 2703 sheet: -0.03 (0.16), residues: 1004 loop : -0.89 (0.10), residues: 3673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 120 HIS 0.007 0.001 HIS a 40 PHE 0.023 0.002 PHE d 52 TYR 0.022 0.002 TYR D 44 ARG 0.007 0.001 ARG Y 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1029 time to evaluate : 7.452 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: A 28 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: A 74 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 102 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8721 (pt) REVERT: B 198 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7546 (ttt-90) REVERT: B 361 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: C 65 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7224 (mm-30) REVERT: C 158 VAL cc_start: 0.8561 (m) cc_final: 0.8343 (m) REVERT: D 178 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7937 (ttpt) REVERT: D 208 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7180 (mtp) REVERT: E 68 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6348 (mttm) REVERT: E 241 GLN cc_start: 0.6474 (OUTLIER) cc_final: 0.6235 (tt0) REVERT: F 108 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7165 (ptp90) REVERT: F 202 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6539 (mpt-90) REVERT: G 206 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: I 123 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6726 (tp-100) REVERT: I 210 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7452 (mtt180) REVERT: J 83 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8193 (tm) REVERT: L 175 ASN cc_start: 0.6936 (m-40) cc_final: 0.6654 (m-40) REVERT: M 17 PHE cc_start: 0.8515 (p90) cc_final: 0.8267 (p90) REVERT: N 9 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: N 104 GLU cc_start: 0.7768 (tt0) cc_final: 0.7516 (tt0) REVERT: O 162 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: O 169 ARG cc_start: 0.7468 (ttm170) cc_final: 0.7229 (mtm180) REVERT: O 178 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7678 (tpp-160) REVERT: O 196 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8236 (mp) REVERT: P 43 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: P 72 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: Q 17 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: R 98 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7750 (ttt180) REVERT: R 114 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7362 (ttpt) REVERT: T 70 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.6145 (p90) REVERT: T 146 LYS cc_start: 0.6882 (mtmm) cc_final: 0.6284 (mttt) REVERT: X 62 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7389 (mmp-170) REVERT: Z 21 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7401 (mpp-170) REVERT: Z 48 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7594 (ptt-90) REVERT: Z 108 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7264 (ptp-110) REVERT: a 27 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8334 (mmmm) REVERT: b 21 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6031 (mt) REVERT: d 56 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: h 111 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: h 116 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7188 (mt) REVERT: i 55 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7840 (mtp180) REVERT: i 56 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: j 13 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8098 (m110) REVERT: k 12 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7984 (mp) REVERT: m 106 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7861 (mmm160) REVERT: n 6 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7699 (ttm-80) REVERT: n 12 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6980 (mtt90) REVERT: o 82 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7724 (mmp) REVERT: u 64 ASN cc_start: 0.3233 (OUTLIER) cc_final: 0.2588 (m-40) REVERT: u 106 VAL cc_start: 0.1773 (OUTLIER) cc_final: 0.1174 (t) REVERT: u 124 LYS cc_start: 0.3365 (OUTLIER) cc_final: 0.2931 (tptm) REVERT: x 73 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8240 (tttp) REVERT: x 157 ILE cc_start: 0.4004 (OUTLIER) cc_final: 0.3389 (tp) REVERT: x 446 MET cc_start: 0.4447 (mmm) cc_final: 0.3974 (mmt) REVERT: x 477 MET cc_start: 0.5784 (mmp) cc_final: 0.4270 (pmm) outliers start: 400 outliers final: 190 residues processed: 1277 average time/residue: 2.2151 time to fit residues: 4057.7239 Evaluate side-chains 1187 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 951 time to evaluate : 7.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 135 ASN Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 62 ARG Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain n residue 10 MET Chi-restraints excluded: chain n residue 12 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 50 LYS Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 124 LYS Chi-restraints excluded: chain u residue 184 SER Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain x residue 23 ILE Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 73 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 88 ASP Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 340 MET Chi-restraints excluded: chain x residue 360 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 1012 optimal weight: 5.9990 chunk 770 optimal weight: 1.9990 chunk 531 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 488 optimal weight: 1.9990 chunk 687 optimal weight: 5.9990 chunk 1028 optimal weight: 10.0000 chunk 1088 optimal weight: 7.9990 chunk 537 optimal weight: 7.9990 chunk 974 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN D 282 GLN F 165 ASN F 241 GLN G 85 GLN L 104 ASN L 111 GLN L 159 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN Y 14 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN h 20 GLN j 76 HIS l 33 ASN m 84 GLN m 120 ASN q 43 ASN r 30 ASN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 232 GLN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 157879 Z= 0.291 Angle : 0.677 11.269 232543 Z= 0.345 Chirality : 0.040 0.357 28938 Planarity : 0.006 0.114 14466 Dihedral : 24.679 179.784 72289 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 6.43 % Allowed : 17.24 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.10), residues: 7380 helix: 1.38 (0.10), residues: 2701 sheet: -0.03 (0.16), residues: 1001 loop : -1.03 (0.10), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.009 0.001 HIS P 145 PHE 0.022 0.002 PHE d 52 TYR 0.024 0.002 TYR D 44 ARG 0.007 0.001 ARG t 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 988 time to evaluate : 7.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7247 (ptm160) REVERT: A 74 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: A 150 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 70 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8259 (mptp) REVERT: B 198 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7540 (ttt-90) REVERT: B 213 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: C 65 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 325 MET cc_start: 0.8762 (tpp) cc_final: 0.8395 (tpt) REVERT: D 178 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7975 (ttpt) REVERT: D 225 GLN cc_start: 0.7550 (tp40) cc_final: 0.7262 (tp40) REVERT: E 67 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.5323 (mtt180) REVERT: E 68 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6397 (mmtm) REVERT: E 228 ILE cc_start: -0.0231 (OUTLIER) cc_final: -0.0689 (mt) REVERT: F 202 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6689 (mpt-90) REVERT: H 163 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8452 (mt0) REVERT: I 35 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7508 (p0) REVERT: I 36 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (pp) REVERT: I 56 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: I 123 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6759 (tp-100) REVERT: I 210 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7423 (mtt180) REVERT: J 83 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8241 (tm) REVERT: J 113 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6320 (pt) REVERT: L 171 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6142 (tp30) REVERT: N 9 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: N 61 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8555 (mt) REVERT: O 113 ASP cc_start: 0.8209 (p0) cc_final: 0.7920 (p0) REVERT: O 162 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: O 169 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7249 (mtm180) REVERT: O 178 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7651 (tpp-160) REVERT: O 196 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8272 (mp) REVERT: P 25 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8959 (m170) REVERT: P 126 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (ttp-170) REVERT: R 28 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6737 (mm-30) REVERT: R 98 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7651 (ttt180) REVERT: R 114 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7528 (ttpt) REVERT: R 144 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6809 (tppt) REVERT: S 96 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: T 70 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.6247 (p90) REVERT: T 146 LYS cc_start: 0.7109 (mtmm) cc_final: 0.6624 (ttmt) REVERT: X 62 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7397 (mmp-170) REVERT: X 144 TYR cc_start: 0.7401 (m-80) cc_final: 0.7160 (m-80) REVERT: Y 126 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7932 (ttp80) REVERT: Z 21 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7549 (mpp-170) REVERT: Z 48 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7703 (ptt-90) REVERT: Z 108 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7330 (ptp-110) REVERT: a 27 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8371 (mmmm) REVERT: b 21 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6325 (mt) REVERT: d 23 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (ptp90) REVERT: d 24 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7817 (tt0) REVERT: d 64 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8839 (mm) REVERT: f 104 MET cc_start: 0.8465 (mmt) cc_final: 0.8048 (mmt) REVERT: g 32 TYR cc_start: 0.8976 (m-10) cc_final: 0.8723 (m-10) REVERT: h 102 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8875 (mp) REVERT: h 107 GLN cc_start: 0.8444 (tp40) cc_final: 0.8113 (tt0) REVERT: h 111 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: h 116 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7360 (mt) REVERT: i 56 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7688 (ttt90) REVERT: j 13 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8156 (m110) REVERT: k 9 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5642 (mtpp) REVERT: k 12 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8029 (mp) REVERT: k 16 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: k 27 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7692 (mppt) REVERT: l 45 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6749 (mmt-90) REVERT: m 106 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7676 (mtt180) REVERT: n 12 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7048 (mtt90) REVERT: o 27 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7291 (mtpp) REVERT: o 82 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7810 (mmp) REVERT: u 4 GLU cc_start: 0.4041 (mm-30) cc_final: 0.3803 (tp30) REVERT: u 64 ASN cc_start: 0.3186 (OUTLIER) cc_final: 0.2652 (m-40) REVERT: u 106 VAL cc_start: 0.1812 (OUTLIER) cc_final: 0.1212 (t) REVERT: u 124 LYS cc_start: 0.3169 (OUTLIER) cc_final: 0.2863 (tptm) REVERT: x 73 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (tttp) REVERT: x 109 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3750 (pp) REVERT: x 157 ILE cc_start: 0.3754 (OUTLIER) cc_final: 0.3188 (tp) REVERT: x 221 MET cc_start: 0.3022 (mpp) cc_final: 0.2743 (ttm) REVERT: x 446 MET cc_start: 0.4530 (mmm) cc_final: 0.4259 (mmt) REVERT: x 477 MET cc_start: 0.5619 (mmp) cc_final: 0.4284 (pmm) REVERT: z 580 MET cc_start: 0.1254 (ttt) cc_final: 0.0185 (tpt) outliers start: 413 outliers final: 206 residues processed: 1253 average time/residue: 2.2034 time to fit residues: 3950.6953 Evaluate side-chains 1195 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 929 time to evaluate : 7.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 187 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 93 LYS Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 111 GLU Chi-restraints excluded: chain V residue 135 ASN Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 62 ARG Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 102 LEU Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain n residue 12 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 102 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 124 LYS Chi-restraints excluded: chain u residue 184 SER Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 73 LYS Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 88 ASP Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 170 ILE Chi-restraints excluded: chain x residue 188 ILE Chi-restraints excluded: chain x residue 340 MET Chi-restraints excluded: chain x residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 906 optimal weight: 4.9990 chunk 617 optimal weight: 5.9990 chunk 15 optimal weight: 50.0000 chunk 810 optimal weight: 4.9990 chunk 449 optimal weight: 3.9990 chunk 928 optimal weight: 5.9990 chunk 752 optimal weight: 2.9990 chunk 1 optimal weight: 40.0000 chunk 555 optimal weight: 10.0000 chunk 976 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN E 178 ASN F 41 GLN F 165 ASN G 206 GLN L 104 ASN L 159 ASN ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 ASN O 50 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 GLN V 36 ASN X 73 HIS X 125 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN a 67 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN h 20 GLN j 76 HIS m 84 GLN q 59 ASN r 30 ASN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 186 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 157879 Z= 0.276 Angle : 0.658 10.452 232543 Z= 0.336 Chirality : 0.040 0.343 28938 Planarity : 0.005 0.103 14466 Dihedral : 24.668 179.759 72285 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 6.62 % Allowed : 17.82 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7380 helix: 1.36 (0.10), residues: 2701 sheet: -0.07 (0.16), residues: 1010 loop : -1.06 (0.10), residues: 3669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 209 HIS 0.011 0.001 HIS B 55 PHE 0.023 0.002 PHE Q 123 TYR 0.027 0.002 TYR U 90 ARG 0.008 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 969 time to evaluate : 7.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7289 (ptm160) REVERT: A 74 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7528 (mm-30) REVERT: A 150 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 66 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7843 (mttt) REVERT: B 198 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7400 (ttt-90) REVERT: C 65 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 325 MET cc_start: 0.8741 (tpp) cc_final: 0.8398 (tpt) REVERT: D 138 GLN cc_start: 0.6204 (mm-40) cc_final: 0.5853 (mm110) REVERT: D 178 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7910 (ttpt) REVERT: E 66 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6920 (ptmm) REVERT: E 67 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5276 (mtt180) REVERT: E 68 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6614 (mmtm) REVERT: F 202 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6301 (mpt-90) REVERT: I 35 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7420 (p0) REVERT: I 36 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8360 (pp) REVERT: I 56 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: I 123 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6749 (tp-100) REVERT: I 210 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7367 (mtt180) REVERT: J 83 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (tm) REVERT: J 113 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6288 (pt) REVERT: L 171 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: N 9 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: O 113 ASP cc_start: 0.8189 (p0) cc_final: 0.7902 (p0) REVERT: O 162 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: O 178 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7685 (tpp-160) REVERT: O 196 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8225 (mp) REVERT: P 25 HIS cc_start: 0.9161 (OUTLIER) cc_final: 0.8951 (m170) REVERT: P 126 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7696 (ttp-170) REVERT: R 28 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6783 (mm-30) REVERT: R 98 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7725 (ttt180) REVERT: R 114 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7701 (ttpt) REVERT: R 144 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7151 (tppt) REVERT: S 96 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: T 70 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.6205 (p90) REVERT: T 146 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6733 (ttmt) REVERT: V 73 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8023 (mtm110) REVERT: X 144 TYR cc_start: 0.7489 (m-80) cc_final: 0.6947 (m-80) REVERT: Y 110 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7270 (tmtm) REVERT: Y 126 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7870 (ttp80) REVERT: Z 21 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7442 (mpp-170) REVERT: Z 48 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (ptt-90) REVERT: Z 108 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7303 (ptp-110) REVERT: Z 132 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: a 27 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8341 (mmmm) REVERT: b 21 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6278 (mt) REVERT: c 36 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7586 (ttmt) REVERT: d 23 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: e 82 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8246 (t) REVERT: f 29 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8613 (tttt) REVERT: h 102 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8823 (mp) REVERT: h 107 GLN cc_start: 0.8449 (tp40) cc_final: 0.8125 (tt0) REVERT: h 111 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: h 116 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7405 (mt) REVERT: i 55 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: i 56 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7709 (ttt90) REVERT: j 13 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (m110) REVERT: k 9 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5670 (mtpp) REVERT: k 12 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7930 (mp) REVERT: k 16 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6801 (mtm180) REVERT: k 27 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7712 (mppt) REVERT: m 106 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7623 (mtt180) REVERT: n 12 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7028 (mtt90) REVERT: o 27 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7328 (mtpp) REVERT: o 82 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7836 (mmp) REVERT: u 98 LEU cc_start: 0.2269 (OUTLIER) cc_final: 0.1933 (tt) REVERT: u 124 LYS cc_start: 0.3326 (OUTLIER) cc_final: 0.2996 (tptm) REVERT: x 73 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (tttp) REVERT: x 157 ILE cc_start: 0.3845 (OUTLIER) cc_final: 0.3128 (tp) REVERT: x 182 GLU cc_start: 0.3565 (OUTLIER) cc_final: 0.0667 (mp0) REVERT: x 221 MET cc_start: 0.3122 (mpp) cc_final: 0.2759 (ttt) REVERT: x 446 MET cc_start: 0.4379 (mmm) cc_final: 0.4068 (mmt) REVERT: x 466 MET cc_start: 0.4002 (ptm) cc_final: 0.3306 (ttt) REVERT: x 477 MET cc_start: 0.5628 (mmp) cc_final: 0.4293 (pmm) outliers start: 425 outliers final: 228 residues processed: 1251 average time/residue: 2.2242 time to fit residues: 3982.0785 Evaluate side-chains 1204 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 916 time to evaluate : 7.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 187 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 93 LYS Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 135 ASN Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain Z residue 132 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 98 SER Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 102 LEU Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain n residue 12 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 98 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 124 LYS Chi-restraints excluded: chain u residue 184 SER Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain x residue 23 ILE Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 73 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 170 ILE Chi-restraints excluded: chain x residue 182 GLU Chi-restraints excluded: chain x residue 191 THR Chi-restraints excluded: chain x residue 275 THR Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 337 GLN Chi-restraints excluded: chain x residue 355 PHE Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 366 optimal weight: 10.0000 chunk 980 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 639 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 chunk 1089 optimal weight: 3.9990 chunk 904 optimal weight: 5.9990 chunk 504 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 186 ASN B 289 GLN D 122 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 178 ASN F 165 ASN G 206 GLN H 162 GLN H 163 GLN L 104 ASN L 159 ASN M 20 HIS N 87 HIS Q 160 HIS R 158 GLN V 36 ASN Y 14 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN a 67 GLN d 18 ASN d 116 ASN h 20 GLN j 76 HIS k 58 GLN l 38 ASN m 84 GLN r 30 ASN r 70 GLN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 186 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 213 GLN x 278 HIS ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 157879 Z= 0.455 Angle : 0.826 11.942 232543 Z= 0.416 Chirality : 0.048 0.392 28938 Planarity : 0.007 0.116 14466 Dihedral : 24.868 179.993 72277 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.44 % Rotamer: Outliers : 7.24 % Allowed : 18.16 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 7380 helix: 0.84 (0.10), residues: 2720 sheet: -0.27 (0.16), residues: 1002 loop : -1.24 (0.10), residues: 3658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP I 209 HIS 0.015 0.002 HIS B 55 PHE 0.033 0.003 PHE Q 174 TYR 0.030 0.003 TYR U 90 ARG 0.009 0.001 ARG a 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 465 poor density : 949 time to evaluate : 7.472 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: A 28 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7228 (ptm160) REVERT: A 74 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 66 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (mttt) REVERT: B 198 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7588 (ttt-90) REVERT: B 280 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 293 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7585 (tt) REVERT: C 201 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6986 (mtt90) REVERT: C 325 MET cc_start: 0.8748 (tpp) cc_final: 0.8463 (tpt) REVERT: D 112 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6619 (tpt-90) REVERT: D 178 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: E 66 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7003 (ptmm) REVERT: E 67 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5348 (mtt180) REVERT: E 68 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6717 (mmtm) REVERT: H 189 GLN cc_start: 0.6104 (OUTLIER) cc_final: 0.5899 (tp40) REVERT: I 35 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7404 (p0) REVERT: I 36 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8538 (pp) REVERT: I 123 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6959 (tp-100) REVERT: I 210 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7525 (mtt180) REVERT: J 67 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7225 (mtmt) REVERT: J 83 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8280 (tm) REVERT: J 113 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6337 (pt) REVERT: L 171 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: M 118 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: N 9 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: N 96 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8181 (mtm-85) REVERT: O 113 ASP cc_start: 0.8232 (p0) cc_final: 0.7947 (p0) REVERT: O 117 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8394 (ptt-90) REVERT: O 178 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7656 (tpp-160) REVERT: O 196 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8281 (mp) REVERT: P 126 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7683 (ttp-170) REVERT: R 98 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7884 (ttt180) REVERT: R 114 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7763 (ttpt) REVERT: S 96 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: T 70 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.6390 (p90) REVERT: V 73 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8231 (mtm110) REVERT: X 144 TYR cc_start: 0.7519 (m-80) cc_final: 0.7000 (m-80) REVERT: Y 126 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7693 (ttp80) REVERT: Z 30 ASP cc_start: 0.7616 (p0) cc_final: 0.7408 (p0) REVERT: Z 48 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7821 (ptt-90) REVERT: Z 108 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7350 (ptp-110) REVERT: a 27 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8401 (mmmm) REVERT: a 134 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: b 21 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6605 (mt) REVERT: c 36 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7673 (ttmt) REVERT: d 20 VAL cc_start: 0.8237 (t) cc_final: 0.8031 (t) REVERT: d 23 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8142 (ptp90) REVERT: d 64 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8794 (mm) REVERT: e 82 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8143 (m) REVERT: f 29 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8557 (tttt) REVERT: h 7 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6621 (mtt90) REVERT: h 102 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8805 (mp) REVERT: h 107 GLN cc_start: 0.8504 (tt0) cc_final: 0.8208 (tt0) REVERT: h 111 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: h 116 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7527 (mt) REVERT: i 56 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7767 (ttt90) REVERT: j 13 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8194 (m110) REVERT: k 9 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5826 (mtpp) REVERT: k 27 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7610 (mppt) REVERT: m 106 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7554 (mtt180) REVERT: n 12 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7153 (mtt90) REVERT: n 23 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6156 (ttm-80) REVERT: o 27 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7325 (mtpp) REVERT: o 59 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8265 (tttp) REVERT: o 82 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7902 (mmp) REVERT: r 20 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7767 (ptt180) REVERT: s 38 ILE cc_start: 0.7512 (pp) cc_final: 0.7300 (pt) REVERT: u 98 LEU cc_start: 0.2387 (OUTLIER) cc_final: 0.2019 (tt) REVERT: u 124 LYS cc_start: 0.3301 (OUTLIER) cc_final: 0.3095 (tttm) REVERT: x 73 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (tttp) REVERT: x 157 ILE cc_start: 0.3849 (OUTLIER) cc_final: 0.3148 (tp) REVERT: x 182 GLU cc_start: 0.4085 (OUTLIER) cc_final: 0.1037 (mp0) REVERT: x 221 MET cc_start: 0.3479 (mpp) cc_final: 0.3103 (ttt) REVERT: x 466 MET cc_start: 0.4178 (ptm) cc_final: 0.3772 (ttt) REVERT: x 477 MET cc_start: 0.5734 (mmp) cc_final: 0.4248 (pmm) REVERT: z 580 MET cc_start: 0.2056 (ttt) cc_final: 0.1835 (mtm) outliers start: 465 outliers final: 253 residues processed: 1257 average time/residue: 2.2223 time to fit residues: 4016.0343 Evaluate side-chains 1235 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 919 time to evaluate : 6.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 189 GLN Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 118 MET Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 187 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 93 LYS Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 ASN Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 102 LEU Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 10 LYS Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain m residue 108 VAL Chi-restraints excluded: chain n residue 12 ARG Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain o residue 57 ARG Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 20 ARG Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 56 ASP Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 70 GLN Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain t residue 81 MET Chi-restraints excluded: chain u residue 3 LEU Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 98 LEU Chi-restraints excluded: chain u residue 102 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 124 LYS Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain w residue 66 HIS Chi-restraints excluded: chain x residue 23 ILE Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 73 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 170 ILE Chi-restraints excluded: chain x residue 182 GLU Chi-restraints excluded: chain x residue 188 ILE Chi-restraints excluded: chain x residue 218 VAL Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 337 GLN Chi-restraints excluded: chain x residue 355 PHE Chi-restraints excluded: chain x residue 437 ILE Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 1050 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 620 optimal weight: 0.0070 chunk 795 optimal weight: 3.9990 chunk 616 optimal weight: 3.9990 chunk 917 optimal weight: 2.9990 chunk 608 optimal weight: 0.9990 chunk 1085 optimal weight: 8.9990 chunk 679 optimal weight: 9.9990 chunk 661 optimal weight: 1.9990 chunk 501 optimal weight: 4.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 289 GLN B 302 ASN D 250 ASN E 178 ASN E 241 GLN F 26 ASN F 165 ASN G 206 GLN L 27 ASN L 104 ASN L 159 ASN M 70 GLN P 80 GLN R 39 GLN U 50 ASN U 105 ASN V 36 ASN V 50 ASN W 59 HIS X 125 ASN Y 14 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN a 67 GLN a 120 GLN b 60 ASN d 18 ASN d 100 ASN f 20 ASN g 112 GLN h 20 GLN j 76 HIS k 58 GLN m 84 GLN r 30 ASN r 70 GLN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 34 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 157879 Z= 0.165 Angle : 0.604 15.520 232543 Z= 0.309 Chirality : 0.036 0.350 28938 Planarity : 0.005 0.101 14466 Dihedral : 24.668 179.557 72277 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 5.28 % Allowed : 20.78 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % 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: -0.02 (0.10), residues: 7380 helix: 1.37 (0.10), residues: 2714 sheet: -0.13 (0.16), residues: 988 loop : -1.05 (0.10), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 209 HIS 0.013 0.001 HIS B 55 PHE 0.017 0.001 PHE x 282 TYR 0.027 0.001 TYR D 44 ARG 0.010 0.000 ARG r 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 985 time to evaluate : 7.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7226 (ptm160) REVERT: A 74 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: B 66 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7781 (mttt) REVERT: B 198 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7320 (ttt-90) REVERT: B 348 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8552 (tmm-80) REVERT: C 65 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 325 MET cc_start: 0.8728 (tpp) cc_final: 0.8354 (tpt) REVERT: D 178 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7961 (ttpt) REVERT: E 67 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.5117 (mtt180) REVERT: F 202 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6615 (mpt-90) REVERT: I 36 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8328 (pp) REVERT: I 56 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: I 123 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6802 (tp-100) REVERT: I 210 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: J 83 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8193 (tm) REVERT: L 171 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: N 9 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: O 113 ASP cc_start: 0.8132 (p0) cc_final: 0.7862 (p0) REVERT: O 178 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7436 (tpp80) REVERT: O 196 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8182 (mp) REVERT: P 25 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8910 (m170) REVERT: R 98 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: R 114 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7646 (ttpt) REVERT: R 163 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.4835 (mmt-90) REVERT: S 96 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: T 70 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.6296 (p90) REVERT: T 79 GLN cc_start: 0.8171 (tt0) cc_final: 0.7898 (tt0) REVERT: T 115 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7403 (mtmt) REVERT: T 146 LYS cc_start: 0.6967 (mtmm) cc_final: 0.6418 (ttmt) REVERT: V 73 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8011 (mtm180) REVERT: X 144 TYR cc_start: 0.7478 (m-80) cc_final: 0.6837 (m-80) REVERT: Y 126 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: Z 21 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7439 (mpp-170) REVERT: Z 48 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7685 (ptp-170) REVERT: Z 108 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7195 (ptp-110) REVERT: a 27 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8293 (mmmm) REVERT: b 21 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6185 (mt) REVERT: d 20 VAL cc_start: 0.7888 (t) cc_final: 0.7684 (t) REVERT: d 23 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8087 (ptp90) REVERT: e 82 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8131 (m) REVERT: f 29 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8604 (tttt) REVERT: f 104 MET cc_start: 0.8531 (mmt) cc_final: 0.7993 (mmt) REVERT: h 107 GLN cc_start: 0.8393 (tt0) cc_final: 0.8109 (tt0) REVERT: h 111 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: i 56 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7667 (ttt90) REVERT: k 27 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7606 (mppt) REVERT: m 119 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7445 (t0) REVERT: n 22 GLN cc_start: 0.8023 (tp40) cc_final: 0.7744 (tp-100) REVERT: o 27 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7348 (mtpp) REVERT: o 82 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7766 (mmp) REVERT: q 67 MET cc_start: 0.3809 (tpp) cc_final: 0.3340 (tpp) REVERT: r 20 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7654 (ptt-90) REVERT: r 70 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7114 (mt0) REVERT: s 28 ILE cc_start: 0.4578 (OUTLIER) cc_final: 0.4077 (pt) REVERT: u 98 LEU cc_start: 0.2071 (OUTLIER) cc_final: 0.1823 (tt) REVERT: u 139 MET cc_start: 0.0558 (tpt) cc_final: 0.0358 (mmm) REVERT: w 19 LEU cc_start: 0.1688 (OUTLIER) cc_final: 0.1102 (mm) REVERT: w 73 MET cc_start: 0.5149 (tpt) cc_final: 0.4679 (tpt) REVERT: x 221 MET cc_start: 0.3244 (mpp) cc_final: 0.2924 (ttt) REVERT: x 382 MET cc_start: 0.3724 (mmp) cc_final: 0.3307 (mmt) REVERT: x 466 MET cc_start: 0.4193 (ptm) cc_final: 0.3494 (ttt) REVERT: x 477 MET cc_start: 0.5505 (mmp) cc_final: 0.4281 (pmm) REVERT: z 580 MET cc_start: 0.2485 (ttt) cc_final: 0.2218 (mtm) outliers start: 339 outliers final: 165 residues processed: 1202 average time/residue: 2.1770 time to fit residues: 3761.6576 Evaluate side-chains 1152 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 943 time to evaluate : 7.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain S residue 16 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 37 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 10 LYS Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain o residue 69 ARG Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 5 LEU Chi-restraints excluded: chain r residue 20 ARG Chi-restraints excluded: chain r residue 70 GLN Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain t residue 81 MET Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 98 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 218 VAL Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 352 ILE Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 671 optimal weight: 0.7980 chunk 433 optimal weight: 8.9990 chunk 648 optimal weight: 7.9990 chunk 326 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 689 optimal weight: 6.9990 chunk 739 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 853 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN C 231 ASN E 178 ASN E 241 GLN F 165 ASN H 163 GLN I 202 ASN L 104 ASN L 111 GLN L 159 ASN P 80 GLN R 158 GLN V 36 ASN V 135 ASN X 93 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Z 132 GLN a 67 GLN b 60 ASN d 18 ASN e 57 ASN h 20 GLN j 13 ASN j 76 HIS k 58 GLN m 84 GLN r 30 ASN r 70 GLN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 157879 Z= 0.337 Angle : 0.719 14.172 232543 Z= 0.365 Chirality : 0.043 0.366 28938 Planarity : 0.006 0.109 14466 Dihedral : 24.707 179.858 72275 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.60 % Rotamer: Outliers : 5.86 % Allowed : 20.56 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7380 helix: 1.18 (0.10), residues: 2708 sheet: -0.21 (0.16), residues: 1002 loop : -1.14 (0.10), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 209 HIS 0.013 0.002 HIS B 55 PHE 0.027 0.002 PHE h 72 TYR 0.030 0.002 TYR U 90 ARG 0.010 0.001 ARG r 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 933 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: A 74 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: B 66 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7975 (mttt) REVERT: B 198 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7509 (ttt-90) REVERT: B 348 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8684 (tmm-80) REVERT: C 325 MET cc_start: 0.8754 (tpp) cc_final: 0.8453 (tpt) REVERT: D 178 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7972 (ttpt) REVERT: E 67 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5304 (mtt180) REVERT: F 33 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7047 (tppt) REVERT: F 108 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: H 71 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (ttt90) REVERT: H 189 GLN cc_start: 0.5846 (OUTLIER) cc_final: 0.5550 (tp40) REVERT: I 35 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7434 (p0) REVERT: I 36 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8383 (pp) REVERT: I 56 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: I 123 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6866 (tp-100) REVERT: I 142 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7026 (mp) REVERT: I 210 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: J 68 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7755 (tp) REVERT: J 83 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8219 (tm) REVERT: L 171 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: N 9 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: O 113 ASP cc_start: 0.8204 (p0) cc_final: 0.7930 (p0) REVERT: O 117 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8344 (ptt-90) REVERT: O 174 LEU cc_start: 0.8708 (tp) cc_final: 0.8396 (mt) REVERT: O 178 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7663 (tpp-160) REVERT: O 196 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8246 (mp) REVERT: R 98 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7704 (ttt180) REVERT: R 114 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7721 (ttpt) REVERT: R 163 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.4933 (mmt-90) REVERT: S 96 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: T 70 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.6304 (p90) REVERT: T 146 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6506 (ttmt) REVERT: U 52 LYS cc_start: 0.6663 (pttt) cc_final: 0.6268 (ptmm) REVERT: V 73 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8052 (mtm110) REVERT: X 144 TYR cc_start: 0.7531 (m-80) cc_final: 0.7031 (m-80) REVERT: Y 126 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: Z 48 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7716 (ptt-90) REVERT: Z 108 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7398 (ptp-110) REVERT: a 27 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8363 (mmmm) REVERT: b 21 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6423 (mt) REVERT: c 36 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7661 (ttmt) REVERT: d 23 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8138 (ptp90) REVERT: d 64 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8766 (mm) REVERT: e 82 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8133 (m) REVERT: f 29 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8592 (tttt) REVERT: h 102 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8833 (mp) REVERT: h 107 GLN cc_start: 0.8476 (tt0) cc_final: 0.8192 (tt0) REVERT: h 111 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: i 55 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7817 (mtp180) REVERT: i 56 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7706 (ttt90) REVERT: k 9 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5746 (mtpp) REVERT: k 27 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7634 (mppt) REVERT: n 23 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8108 (ttm170) REVERT: o 27 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7359 (mtpp) REVERT: o 59 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8258 (tttp) REVERT: o 82 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7812 (mmp) REVERT: q 67 MET cc_start: 0.4119 (tpp) cc_final: 0.3730 (tpp) REVERT: r 20 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7730 (ptt180) REVERT: r 46 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7838 (mtt-85) REVERT: s 28 ILE cc_start: 0.4826 (OUTLIER) cc_final: 0.4323 (pt) REVERT: s 38 ILE cc_start: 0.7575 (pp) cc_final: 0.7281 (pt) REVERT: u 98 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.1830 (tt) REVERT: x 157 ILE cc_start: 0.3661 (OUTLIER) cc_final: 0.3070 (tp) REVERT: x 182 GLU cc_start: 0.3980 (OUTLIER) cc_final: 0.0896 (mp0) REVERT: x 205 MET cc_start: 0.4065 (mtp) cc_final: 0.3571 (mmm) REVERT: x 221 MET cc_start: 0.3223 (mpp) cc_final: 0.2972 (ttt) REVERT: x 466 MET cc_start: 0.4304 (ptm) cc_final: 0.3666 (ttt) REVERT: x 477 MET cc_start: 0.5678 (mmp) cc_final: 0.4257 (pmm) REVERT: z 580 MET cc_start: 0.2593 (ttt) cc_final: 0.2310 (mtm) outliers start: 376 outliers final: 221 residues processed: 1184 average time/residue: 2.2317 time to fit residues: 3792.2279 Evaluate side-chains 1185 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 908 time to evaluate : 7.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 189 GLN Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain S residue 16 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 93 LYS Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 75 LEU Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 102 ASN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 65 MET Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 102 LEU Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 10 LYS Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain o residue 57 ARG Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 69 ARG Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 96 ASP Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 20 ARG Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain t residue 81 MET Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 98 LEU Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 184 SER Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain w residue 66 HIS Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 170 ILE Chi-restraints excluded: chain x residue 182 GLU Chi-restraints excluded: chain x residue 188 ILE Chi-restraints excluded: chain x residue 218 VAL Chi-restraints excluded: chain x residue 319 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 352 ILE Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 987 optimal weight: 2.9990 chunk 1039 optimal weight: 8.9990 chunk 948 optimal weight: 2.9990 chunk 1011 optimal weight: 6.9990 chunk 608 optimal weight: 0.8980 chunk 440 optimal weight: 3.9990 chunk 794 optimal weight: 7.9990 chunk 310 optimal weight: 10.0000 chunk 913 optimal weight: 0.3980 chunk 956 optimal weight: 6.9990 chunk 1007 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 302 ASN E 153 HIS E 241 GLN F 165 ASN G 64 GLN H 163 GLN I 202 ASN L 104 ASN L 111 GLN L 159 ASN P 25 HIS P 80 GLN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN V 135 ASN X 93 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Z 132 GLN a 67 GLN b 60 ASN d 18 ASN h 20 GLN j 13 ASN j 76 HIS m 84 GLN r 30 ASN r 70 GLN r 83 ASN r 103 HIS ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 207 GLN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 157879 Z= 0.171 Angle : 0.601 12.786 232543 Z= 0.309 Chirality : 0.036 0.386 28938 Planarity : 0.005 0.100 14466 Dihedral : 24.616 179.664 72275 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 4.70 % Allowed : 21.76 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 7380 helix: 1.45 (0.10), residues: 2717 sheet: -0.15 (0.16), residues: 992 loop : -1.02 (0.10), residues: 3671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP I 209 HIS 0.010 0.001 HIS B 55 PHE 0.027 0.001 PHE x 359 TYR 0.024 0.001 TYR D 44 ARG 0.012 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 957 time to evaluate : 7.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7319 (ptm160) REVERT: A 74 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: B 34 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8274 (mtpp) REVERT: B 66 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7761 (mttt) REVERT: B 198 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7306 (ttt-90) REVERT: C 325 MET cc_start: 0.8722 (tpp) cc_final: 0.8351 (tpt) REVERT: D 178 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: F 33 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6878 (tppt) REVERT: F 108 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7014 (ptp90) REVERT: F 202 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6628 (mpt-90) REVERT: H 92 MET cc_start: 0.8414 (ptm) cc_final: 0.8201 (ptm) REVERT: I 35 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7466 (p0) REVERT: I 36 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8304 (pp) REVERT: I 56 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: I 123 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6846 (tp-100) REVERT: I 210 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7394 (mtt180) REVERT: J 68 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7546 (tp) REVERT: J 83 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8188 (tm) REVERT: L 171 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: N 9 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: N 61 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (mt) REVERT: O 113 ASP cc_start: 0.8134 (p0) cc_final: 0.7852 (p0) REVERT: O 117 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8354 (ptt-90) REVERT: O 162 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: O 174 LEU cc_start: 0.8686 (tp) cc_final: 0.8382 (mt) REVERT: O 178 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7678 (tpp-160) REVERT: O 196 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8130 (mp) REVERT: R 98 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7590 (ttt180) REVERT: R 163 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.4825 (mmt-90) REVERT: S 96 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: T 70 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.6194 (p90) REVERT: T 146 LYS cc_start: 0.7075 (mtmm) cc_final: 0.6508 (ttmt) REVERT: U 52 LYS cc_start: 0.6586 (pttt) cc_final: 0.6231 (ptmm) REVERT: V 73 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8005 (mtm180) REVERT: X 144 TYR cc_start: 0.7507 (m-80) cc_final: 0.6859 (m-80) REVERT: Y 126 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: Z 21 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7401 (mpp-170) REVERT: Z 48 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7640 (ptp-170) REVERT: Z 108 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7254 (ptp-110) REVERT: a 27 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8296 (mmmm) REVERT: b 21 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6210 (mt) REVERT: c 36 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (mttt) REVERT: d 23 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8100 (ptp90) REVERT: f 104 MET cc_start: 0.8541 (mmt) cc_final: 0.8007 (mmt) REVERT: h 102 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8815 (mp) REVERT: h 107 GLN cc_start: 0.8399 (tt0) cc_final: 0.8111 (tt0) REVERT: h 111 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: i 55 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7825 (mtp180) REVERT: i 56 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7655 (ttt90) REVERT: k 9 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5742 (mtpp) REVERT: k 27 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: n 23 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8126 (ttm170) REVERT: o 82 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7801 (mmp) REVERT: q 67 MET cc_start: 0.4176 (tpp) cc_final: 0.3784 (tpp) REVERT: r 20 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7653 (ptt-90) REVERT: r 46 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7590 (mtt-85) REVERT: r 70 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6224 (mt0) REVERT: s 28 ILE cc_start: 0.4709 (OUTLIER) cc_final: 0.4225 (pt) REVERT: s 38 ILE cc_start: 0.7680 (pp) cc_final: 0.7297 (pt) REVERT: w 19 LEU cc_start: 0.1655 (OUTLIER) cc_final: 0.1134 (mm) REVERT: x 157 ILE cc_start: 0.3704 (OUTLIER) cc_final: 0.3169 (tp) REVERT: x 182 GLU cc_start: 0.3796 (OUTLIER) cc_final: 0.0754 (mp0) REVERT: x 205 MET cc_start: 0.4162 (mtp) cc_final: 0.3564 (mmm) REVERT: x 221 MET cc_start: 0.3224 (mpp) cc_final: 0.2926 (ttt) REVERT: x 382 MET cc_start: 0.3840 (OUTLIER) cc_final: 0.3423 (mmt) REVERT: x 466 MET cc_start: 0.4215 (ptm) cc_final: 0.3601 (ttt) REVERT: x 477 MET cc_start: 0.5543 (mmp) cc_final: 0.4270 (pmm) REVERT: z 580 MET cc_start: 0.2516 (ttt) cc_final: 0.2268 (mtm) outliers start: 302 outliers final: 186 residues processed: 1162 average time/residue: 2.2078 time to fit residues: 3682.5380 Evaluate side-chains 1172 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 934 time to evaluate : 7.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain S residue 16 CYS Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 75 LEU Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 102 LEU Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 10 LYS Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 57 ARG Chi-restraints excluded: chain o residue 69 ARG Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain r residue 5 LEU Chi-restraints excluded: chain r residue 20 ARG Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 46 ARG Chi-restraints excluded: chain r residue 70 GLN Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain t residue 81 MET Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 72 MET Chi-restraints excluded: chain u residue 76 ARG Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain w residue 66 HIS Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 182 GLU Chi-restraints excluded: chain x residue 218 VAL Chi-restraints excluded: chain x residue 319 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 352 ILE Chi-restraints excluded: chain x residue 360 MET Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 664 optimal weight: 6.9990 chunk 1069 optimal weight: 0.6980 chunk 652 optimal weight: 0.0050 chunk 507 optimal weight: 9.9990 chunk 743 optimal weight: 0.9990 chunk 1121 optimal weight: 10.0000 chunk 1032 optimal weight: 3.9990 chunk 893 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 689 optimal weight: 3.9990 chunk 547 optimal weight: 3.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 289 GLN B 302 ASN E 241 GLN F 165 ASN H 163 GLN I 202 ASN J 46 GLN L 104 ASN L 111 GLN L 159 ASN L 175 ASN V 36 ASN V 135 ASN X 93 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Z 132 GLN a 67 GLN b 60 ASN d 18 ASN e 24 GLN e 57 ASN h 20 GLN j 76 HIS m 84 GLN r 30 ASN r 83 ASN r 103 HIS ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 157879 Z= 0.158 Angle : 0.577 12.003 232543 Z= 0.295 Chirality : 0.035 0.361 28938 Planarity : 0.004 0.098 14466 Dihedral : 24.528 179.925 72273 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 4.11 % Allowed : 22.51 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 7380 helix: 1.59 (0.10), residues: 2717 sheet: -0.08 (0.16), residues: 995 loop : -0.97 (0.10), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP I 209 HIS 0.008 0.001 HIS B 55 PHE 0.027 0.001 PHE x 359 TYR 0.023 0.001 TYR D 44 ARG 0.009 0.000 ARG h 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 964 time to evaluate : 7.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7611 (mm-30) REVERT: B 66 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7708 (mttt) REVERT: B 198 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7316 (ttt-90) REVERT: C 325 MET cc_start: 0.8704 (tpp) cc_final: 0.8369 (tpt) REVERT: D 178 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: E 108 MET cc_start: 0.6991 (mtp) cc_final: 0.6751 (mmt) REVERT: E 218 LEU cc_start: 0.1844 (OUTLIER) cc_final: 0.1278 (tp) REVERT: F 108 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6994 (ptp90) REVERT: F 202 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6562 (mpt-90) REVERT: H 189 GLN cc_start: 0.5698 (OUTLIER) cc_final: 0.5413 (tp40) REVERT: I 35 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7556 (p0) REVERT: I 36 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8284 (pp) REVERT: I 56 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: I 123 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6788 (tp-100) REVERT: I 210 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: J 68 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7631 (tp) REVERT: J 83 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8154 (tm) REVERT: L 159 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (m-40) REVERT: L 171 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5804 (tp30) REVERT: N 9 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: O 113 ASP cc_start: 0.8138 (p0) cc_final: 0.7867 (p0) REVERT: O 117 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8345 (ptt-90) REVERT: O 162 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: O 174 LEU cc_start: 0.8680 (tp) cc_final: 0.8375 (mt) REVERT: O 178 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7403 (tpp80) REVERT: R 98 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7559 (ttt180) REVERT: R 163 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.4810 (mmt-90) REVERT: S 96 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: T 70 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.6118 (p90) REVERT: T 92 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8613 (ttt-90) REVERT: T 146 LYS cc_start: 0.7054 (mtmm) cc_final: 0.6504 (ttmt) REVERT: U 52 LYS cc_start: 0.6613 (pttt) cc_final: 0.6287 (ptmm) REVERT: V 73 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7985 (mtm180) REVERT: X 144 TYR cc_start: 0.7493 (m-80) cc_final: 0.6845 (m-80) REVERT: Z 21 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7405 (mpp-170) REVERT: Z 48 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7581 (ptp-170) REVERT: Z 84 ARG cc_start: 0.8116 (ptm-80) cc_final: 0.7841 (ptt90) REVERT: Z 108 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7278 (ptp-110) REVERT: a 27 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8269 (mmmm) REVERT: b 21 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.5975 (mt) REVERT: c 36 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8114 (mttt) REVERT: d 23 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: e 82 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7866 (t) REVERT: f 66 LYS cc_start: 0.8188 (mttm) cc_final: 0.7836 (mttt) REVERT: f 104 MET cc_start: 0.8490 (mmt) cc_final: 0.8010 (mmt) REVERT: h 107 GLN cc_start: 0.8383 (tt0) cc_final: 0.8109 (tt0) REVERT: h 111 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: i 55 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7793 (mtp180) REVERT: i 56 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7611 (ttt90) REVERT: k 27 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7608 (mppt) REVERT: n 23 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8223 (ttm170) REVERT: o 82 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7802 (mmp) REVERT: q 67 MET cc_start: 0.4129 (tpp) cc_final: 0.3738 (tpp) REVERT: r 20 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7654 (ptt-90) REVERT: r 121 GLN cc_start: 0.8470 (pt0) cc_final: 0.8184 (mt0) REVERT: s 28 ILE cc_start: 0.4584 (OUTLIER) cc_final: 0.4110 (pt) REVERT: s 38 ILE cc_start: 0.7605 (pp) cc_final: 0.7193 (pt) REVERT: s 82 PHE cc_start: 0.5653 (t80) cc_final: 0.5204 (t80) REVERT: u 139 MET cc_start: 0.0083 (tpt) cc_final: -0.0289 (mmm) REVERT: w 19 LEU cc_start: 0.1648 (OUTLIER) cc_final: 0.1211 (mm) REVERT: x 157 ILE cc_start: 0.3721 (OUTLIER) cc_final: 0.3226 (tp) REVERT: x 205 MET cc_start: 0.4142 (mtp) cc_final: 0.3511 (mmm) REVERT: x 221 MET cc_start: 0.3222 (mpp) cc_final: 0.2939 (ttt) REVERT: x 382 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.3340 (mmt) REVERT: x 466 MET cc_start: 0.4062 (ptm) cc_final: 0.3405 (ttt) REVERT: x 477 MET cc_start: 0.5688 (mmp) cc_final: 0.4168 (pmm) outliers start: 264 outliers final: 172 residues processed: 1131 average time/residue: 2.2507 time to fit residues: 3644.9359 Evaluate side-chains 1148 residues out of total 6444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 930 time to evaluate : 7.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 189 GLN Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain L residue 175 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 178 ARG Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain V residue 73 ARG Chi-restraints excluded: chain V residue 138 SER Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 151 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 21 ARG Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 48 ARG Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 23 ARG Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 SER Chi-restraints excluded: chain g residue 54 ARG Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 103 LYS Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain i residue 55 ARG Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain j residue 10 LYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 27 LYS Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain n residue 23 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 57 ARG Chi-restraints excluded: chain o residue 69 ARG Chi-restraints excluded: chain o residue 82 MET Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain r residue 5 LEU Chi-restraints excluded: chain r residue 20 ARG Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 79 ASN Chi-restraints excluded: chain t residue 81 MET Chi-restraints excluded: chain u residue 3 LEU Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 72 MET Chi-restraints excluded: chain u residue 76 ARG Chi-restraints excluded: chain u residue 90 THR Chi-restraints excluded: chain u residue 106 VAL Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 50 VAL Chi-restraints excluded: chain w residue 66 HIS Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 75 ILE Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 87 VAL Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 157 ILE Chi-restraints excluded: chain x residue 319 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 360 MET Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain z residue 573 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 709 optimal weight: 2.9990 chunk 951 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 823 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 894 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 918 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 167 GLN B 289 GLN E 241 GLN F 165 ASN H 163 GLN I 202 ASN L 104 ASN Q 93 GLN R 158 GLN V 36 ASN V 135 ASN ** Y 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Z 76 ASN Z 132 GLN a 67 GLN b 60 ASN d 18 ASN d 100 ASN h 20 GLN j 76 HIS m 84 GLN r 30 ASN r 83 ASN r 103 HIS ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127564 restraints weight = 177072.549| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.36 r_work: 0.3108 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 157879 Z= 0.332 Angle : 0.643 59.189 232543 Z= 0.339 Chirality : 0.041 1.252 28938 Planarity : 0.005 0.229 14466 Dihedral : 24.525 179.961 72270 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 3.93 % Allowed : 23.01 % Favored : 73.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 7380 helix: 1.58 (0.10), residues: 2711 sheet: -0.07 (0.16), residues: 995 loop : -0.98 (0.10), residues: 3674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 209 HIS 0.010 0.001 HIS B 55 PHE 0.023 0.002 PHE h 72 TYR 0.022 0.002 TYR D 44 ARG 0.008 0.001 ARG h 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52785.34 seconds wall clock time: 915 minutes 49.84 seconds (54949.84 seconds total)