Starting phenix.real_space_refine on Tue Mar 26 03:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt7_23976/03_2024/7mt7_23976_updated.pdb" } resolution = 2.71 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 4912 5.49 5 Mg 443 5.21 5 S 90 5.16 5 C 74293 2.51 5 N 27996 2.21 5 O 41956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149696 Number of models: 1 Model: "" Number of chains: 71 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 446 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 186 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66958 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 1, 'rna2p_pur': 303, 'rna2p_pyr': 155, 'rna3p': 1, 'rna3p_pur': 1479, 'rna3p_pyr': 1179} Link IDs: {'rna2p': 459, 'rna3p': 2658} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 47} Link IDs: {'rna2p': 12, 'rna3p': 102} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 564 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 94, 'rna3p': 6, 'rna3p_pur': 732, 'rna3p_pyr': 568} Link IDs: {'rna2p': 212, 'rna3p': 1306} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "x" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 297 Unusual residues: {' MG': 297} Classifications: {'undetermined': 297} Link IDs: {None: 296} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Unusual residues: {' MG': 129} Classifications: {'undetermined': 129} Link IDs: {None: 128} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 116.960 179.521 186.775 1.00 30.27 S ATOM 519 SG CYS 1 18 117.153 182.668 184.525 1.00 33.97 S ATOM 734 SG CYS 1 42 120.216 181.376 185.759 1.00 22.14 S ATOM 755 SG CYS 1 45 118.316 183.278 188.730 1.00 26.69 S ATOM 1778 SG CYS 4 11 184.518 97.638 135.838 1.00 50.57 S ATOM 1801 SG CYS 4 14 184.698 101.000 134.576 1.00 47.50 S ATOM 1911 SG CYS 4 27 186.243 98.640 132.280 1.00 44.03 S ATOM 2121 SG CYS 6 16 113.295 113.154 222.968 1.00 58.15 S ATOM 2280 SG CYS 6 38 116.916 113.429 223.015 1.00 55.77 S ATOM 2301 SG CYS 6 41 115.193 110.212 221.967 1.00 60.27 S ATOM 94973 SG CYS X 5 91.578 200.506 121.963 1.00 23.36 S ATOM 94995 SG CYS X 8 93.819 202.549 124.236 1.00 27.05 S ATOM 95338 SG CYS X 52 91.338 199.315 125.850 1.00 23.97 S ATOM 95357 SG CYS X 55 89.935 202.526 124.908 1.00 27.63 S ATOM A0VVZ SG CYS n 24 89.094 55.845 169.787 1.00 34.18 S ATOM A0VWK SG CYS n 27 91.149 56.897 166.550 1.00 34.63 S ATOM A0VZI SG CYS n 40 88.308 59.381 168.303 1.00 31.14 S ATOM A0W07 SG CYS n 43 87.305 56.118 166.349 1.00 33.68 S ATOM A0XYE SG CYS r 20 34.761 120.658 107.984 1.00 51.21 S ATOM A0XZ2 SG CYS r 23 34.459 119.410 104.436 1.00 54.49 S ATOM A0Y6N SG CYS r 57 38.115 119.811 105.264 1.00 37.45 S Time building chain proxies: 57.66, per 1000 atoms: 0.39 Number of scatterers: 149696 At special positions: 0 Unit cell: (240.62, 269.24, 242.74, 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 6 29.99 S 90 16.00 P 4912 15.00 Mg 443 11.99 O 41956 8.00 N 27996 7.00 C 74293 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.70 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " Number of angles added : 24 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10258 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: 166 helices and 77 sheets defined 36.9% alpha, 19.3% beta 1471 base pairs and 2780 stacking pairs defined. Time for finding SS restraints: 75.59 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 3.866A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.680A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '1' and resid 28 through 33 Proline residue: 1 33 - end of helix No H-bonds generated for 'chain '1' and resid 28 through 33' Processing helix chain '2' and resid 11 through 19 Processing helix chain '2' and resid 20 through 28 removed outlier: 3.898A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.590A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 45 removed outlier: 3.594A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 4.917A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 3.873A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '6' and resid 56 through 65 Processing helix chain '7' and resid 2 through 14 removed outlier: 3.661A pdb=" N ARG 7 6 " --> pdb=" O ALA 7 2 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 7 11 " --> pdb=" O LYS 7 7 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS 7 12 " --> pdb=" O LYS 7 8 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR 7 13 " --> pdb=" O ARG 7 9 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER 7 14 " --> pdb=" O ASP 7 10 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 16 removed outlier: 3.615A pdb=" N ALA 8 10 " --> pdb=" O LYS 8 6 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA 8 11 " --> pdb=" O ALA 8 7 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS 8 14 " --> pdb=" O ALA 8 10 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 37 removed outlier: 3.542A pdb=" N ALA 8 27 " --> pdb=" O PRO 8 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU 8 32 " --> pdb=" O LYS 8 28 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 3.623A pdb=" N ASP 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA 8 87 " --> pdb=" O LYS 8 83 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 8 89 " --> pdb=" O ASP 8 85 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 107 removed outlier: 3.556A pdb=" N ILE 8 101 " --> pdb=" O SER 8 97 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU 8 102 " --> pdb=" O ASP 8 98 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE 8 104 " --> pdb=" O LEU 8 100 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN 8 105 " --> pdb=" O ILE 8 101 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY 8 106 " --> pdb=" O GLU 8 102 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 125 removed outlier: 3.503A pdb=" N MET 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA 8 122 " --> pdb=" O PRO 8 118 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS 8 123 " --> pdb=" O ASP 8 119 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY 8 125 " --> pdb=" O MET 8 121 " (cutoff:3.500A) Processing helix chain '8' and resid 126 through 132 removed outlier: 4.770A pdb=" N VAL 8 130 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) Processing helix chain '8' and resid 148 through 159 removed outlier: 3.867A pdb=" N ALA 8 152 " --> pdb=" O ASP 8 148 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 3.523A pdb=" N ASN 8 188 " --> pdb=" O LEU 8 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 8 193 " --> pdb=" O TYR 8 189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP 8 194 " --> pdb=" O GLY 8 190 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU 8 195 " --> pdb=" O ALA 8 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU 8 199 " --> pdb=" O GLU 8 195 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS 8 200 " --> pdb=" O VAL 8 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.682A pdb=" N ARG C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLY C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.679A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.851A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.973A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.550A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.618A pdb=" N GLN C 201 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.886A pdb=" N VAL D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.801A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.816A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.517A pdb=" N GLY D 46 " --> pdb=" O THR D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.564A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.273A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.992A pdb=" N ALA E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.620A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.543A pdb=" N ASN E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.671A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 5.704A pdb=" N ASP F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 5.102A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.664A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 removed outlier: 4.188A pdb=" N ILE F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 154' Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.909A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.900A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.785A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 65 through 71 removed outlier: 3.712A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.532A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.544A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.082A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.718A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.456A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.727A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.504A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.557A pdb=" N LYS L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.767A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.753A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.514A pdb=" N THR M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.616A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.663A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.668A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.512A pdb=" N LYS N 68 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.534A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.685A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 3.529A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 69 removed outlier: 3.561A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Proline residue: O 69 - end of helix Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.530A pdb=" N ARG O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU O 85 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.564A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.631A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 97 through 103 removed outlier: 4.781A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 4.379A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.295A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 73 removed outlier: 3.523A pdb=" N GLU Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.523A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.653A pdb=" N VAL Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Proline residue: Q 118 - end of helix Processing helix chain 'R' and resid 52 through 60 removed outlier: 4.568A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.883A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP S 32 " --> pdb=" O ARG S 28 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 3.908A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.624A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.554A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.622A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.237A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 51 removed outlier: 3.611A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.368A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.609A pdb=" N GLY V 29 " --> pdb=" O ALA V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 60 removed outlier: 5.079A pdb=" N TYR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER V 59 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY V 60 " --> pdb=" O LEU V 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 4.502A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.662A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 39 removed outlier: 4.249A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 67 removed outlier: 4.762A pdb=" N LEU Y 47 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.570A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.762A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.659A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.556A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 5.048A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.980A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.837A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.658A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Proline residue: c 144 - end of helix Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.505A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.686A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.574A pdb=" N GLU d 52 " --> pdb=" O LEU d 48 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.597A pdb=" N GLU d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.614A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.575A pdb=" N ALA d 109 " --> pdb=" O THR d 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU d 112 " --> pdb=" O MET d 108 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 146 removed outlier: 5.435A pdb=" N ASN d 146 " --> pdb=" O ASP d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 3.800A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 removed outlier: 6.379A pdb=" N ILE d 186 " --> pdb=" O GLU d 182 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 182 through 187' Processing helix chain 'd' and resid 192 through 201 removed outlier: 4.376A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 3.731A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 3.975A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.633A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.544A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 3.921A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 209 removed outlier: 4.096A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU e 208 " --> pdb=" O ARG e 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 5.106A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.055A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 3.730A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.988A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.524A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.639A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.633A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.576A pdb=" N ASN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.552A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N HIS g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.719A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.509A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.871A pdb=" N ARG h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN h 121 " --> pdb=" O GLN h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.591A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 3.594A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.702A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.693A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.484A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.031A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 3.521A pdb=" N VAL k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 61' Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.654A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.834A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA k 112 " --> pdb=" O ARG k 108 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.620A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.496A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.815A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.503A pdb=" N LEU m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA m 36 " --> pdb=" O GLU m 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.039A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.889A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.497A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE m 82 " --> pdb=" O ILE m 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.589A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.624A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 5.085A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.587A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.207A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.502A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.658A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.658A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 85 Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.513A pdb=" N VAL p 105 " --> pdb=" O SER p 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP p 114 " --> pdb=" O LEU p 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.437A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 42 removed outlier: 3.665A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG r 39 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 34 through 42' Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.645A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.637A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL r 74 " --> pdb=" O ASN r 70 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 4.004A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL s 19 " --> pdb=" O LEU s 15 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 5.044A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 5 through 42 removed outlier: 3.508A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU t 15 " --> pdb=" O ASN t 11 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR t 30 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.652A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU t 51 " --> pdb=" O ALA t 47 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.510A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 Processing sheet with id= 2, first strand: chain '1' and resid 10 through 13 Processing sheet with id= 3, first strand: chain '1' and resid 37 through 40 Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.082A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '4' and resid 1 through 5 removed outlier: 5.636A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '6' and resid 11 through 16 removed outlier: 4.084A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 59 through 64 removed outlier: 6.196A pdb=" N VAL 8 59 " --> pdb=" O VAL 8 165 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 8 161 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '8' and resid 75 through 78 removed outlier: 4.011A pdb=" N ILE 8 115 " --> pdb=" O ALA 8 76 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE 8 78 " --> pdb=" O ILE 8 115 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '8' and resid 169 through 176 removed outlier: 6.246A pdb=" N ALA 8 169 " --> pdb=" O LEU 8 48 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.916A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.800A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 139 through 143 removed outlier: 4.045A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.388A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.736A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.833A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 48 through 54 removed outlier: 5.340A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 109 through 113 removed outlier: 4.239A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.430A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= 21, first strand: chain 'F' and resid 72 through 76 removed outlier: 4.782A pdb=" N VAL F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN F 44 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 23 through 27 removed outlier: 3.506A pdb=" N LEU G 33 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 24, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.623A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= 26, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.344A pdb=" N LEU H 35 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 28, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.245A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.543A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 31, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.814A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 33, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.713A pdb=" N SER L 142 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 38 through 41 removed outlier: 6.596A pdb=" N GLU M 38 " --> pdb=" O PRO M 99 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 62 through 66 removed outlier: 4.023A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= 37, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.542A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.469A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.597A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY P 52 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG P 55 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.773A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'R' and resid 20 through 24 removed outlier: 4.140A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU R 34 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'R' and resid 67 through 71 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'R' and resid 73 through 80 removed outlier: 3.733A pdb=" N LYS R 80 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR R 85 " --> pdb=" O LYS R 80 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.642A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.943A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.529A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.618A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'U' and resid 39 through 42 removed outlier: 5.647A pdb=" N ASN U 39 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA U 64 " --> pdb=" O ASN U 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN U 62 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 50, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.944A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN V 74 " --> pdb=" O LEU V 67 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 42 through 46 removed outlier: 3.612A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'V' and resid 119 through 124 removed outlier: 7.434A pdb=" N ASP V 119 " --> pdb=" O ALA V 182 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA V 182 " --> pdb=" O ASP V 119 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'V' and resid 127 through 132 removed outlier: 6.312A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 55, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.541A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.341A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.020A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.569A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR c 191 " --> pdb=" O GLY c 194 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'd' and resid 136 through 139 removed outlier: 4.378A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.893A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 115 through 119 removed outlier: 5.501A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 64 through 72 removed outlier: 4.926A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.570A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 39 through 43 removed outlier: 3.921A pdb=" N LYS f 39 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP f 64 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'f' and resid 44 through 48 removed outlier: 3.786A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.253A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.563A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.018A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.373A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU i 42 " --> pdb=" O ILE i 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY i 31 " --> pdb=" O VAL i 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY i 89 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG i 39 " --> pdb=" O HIS i 87 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL i 43 " --> pdb=" O ASP i 83 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'j' and resid 7 through 12 removed outlier: 4.046A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 39 through 46 removed outlier: 3.975A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL k 94 " --> pdb=" O GLY k 118 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.005A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.776A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.397A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'q' and resid 58 through 63 removed outlier: 5.394A pdb=" N LYS q 58 " --> pdb=" O GLU q 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 76 Processing sheet with id= 77, first strand: chain 's' and resid 30 through 33 removed outlier: 4.787A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 4545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3700 hydrogen bonds 5896 hydrogen bond angles 0 basepair planarities 1471 basepair parallelities 2780 stacking parallelities Total time for adding SS restraints: 305.52 Time building geometry restraints manager: 66.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12058 1.29 - 1.42: 73340 1.42 - 1.55: 67121 1.55 - 1.68: 9833 1.68 - 1.81: 150 Bond restraints: 162502 Sorted by residual: bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.447 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.596 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C8 G7M a 518 " pdb=" N7 G7M a 518 " ideal model delta sigma weight residual 1.348 1.506 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 1.348 1.499 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N1 5MU A2177 " pdb=" C2 5MU A2177 " ideal model delta sigma weight residual 1.436 1.552 -0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 162497 not shown) Histogram of bond angle deviations from ideal: 97.83 - 106.21: 28875 106.21 - 114.58: 104944 114.58 - 122.96: 81908 122.96 - 131.34: 26943 131.34 - 139.71: 1290 Bond angle restraints: 243960 Sorted by residual: angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 131.55 -23.26 3.00e+00 1.11e-01 6.01e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 120.40 22.42 3.00e+00 1.11e-01 5.59e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C8 2MG a 959 " ideal model delta sigma weight residual 110.07 130.36 -20.29 3.00e+00 1.11e-01 4.58e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C4 2MG a 959 " ideal model delta sigma weight residual 138.70 121.69 17.01 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C PRO p 46 " pdb=" N SER p 47 " pdb=" CA SER p 47 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 ... (remaining 243955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 92530 35.98 - 71.96: 10837 71.96 - 107.94: 1352 107.94 - 143.92: 9 143.92 - 179.90: 34 Dihedral angle restraints: 104762 sinusoidal: 88797 harmonic: 15965 Sorted by residual: dihedral pdb=" CA ALA l 113 " pdb=" C ALA l 113 " pdb=" N ARG l 114 " pdb=" CA ARG l 114 " ideal model delta harmonic sigma weight residual 180.00 131.27 48.73 0 5.00e+00 4.00e-02 9.50e+01 dihedral pdb=" O4' C A1517 " pdb=" C1' C A1517 " pdb=" N1 C A1517 " pdb=" C2 C A1517 " ideal model delta sinusoidal sigma weight residual -160.00 19.90 -179.90 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 739 " pdb=" C1' C A 739 " pdb=" N1 C A 739 " pdb=" C2 C A 739 " ideal model delta sinusoidal sigma weight residual -160.00 19.32 -179.32 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 104759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 29285 0.087 - 0.174: 1850 0.174 - 0.261: 88 0.261 - 0.347: 13 0.347 - 0.434: 3 Chirality restraints: 31239 Sorted by residual: chirality pdb=" CB ILE c 102 " pdb=" CA ILE c 102 " pdb=" CG1 ILE c 102 " pdb=" CG2 ILE c 102 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CB VAL g 75 " pdb=" CA VAL g 75 " pdb=" CG1 VAL g 75 " pdb=" CG2 VAL g 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL Z 50 " pdb=" CA VAL Z 50 " pdb=" CG1 VAL Z 50 " pdb=" CG2 VAL Z 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 31236 not shown) Planarity restraints: 12700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.045 2.00e-02 2.50e+03 5.76e-01 7.45e+03 pdb=" C4' OMG A2791 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.626 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.583 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.926 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.227 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.867 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " 0.056 2.00e-02 2.50e+03 5.36e-01 6.48e+03 pdb=" C4' 2MG a 959 " 0.410 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.500 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.541 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.210 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.908 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.242 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.772 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A2177 " -0.674 2.00e-02 2.50e+03 5.07e-01 5.78e+03 pdb=" C4' 5MU A2177 " 0.239 2.00e-02 2.50e+03 pdb=" O4' 5MU A2177 " 0.442 2.00e-02 2.50e+03 pdb=" C3' 5MU A2177 " -0.227 2.00e-02 2.50e+03 pdb=" O3' 5MU A2177 " 0.883 2.00e-02 2.50e+03 pdb=" C2' 5MU A2177 " -0.607 2.00e-02 2.50e+03 pdb=" O2' 5MU A2177 " -0.497 2.00e-02 2.50e+03 pdb=" C1' 5MU A2177 " 0.397 2.00e-02 2.50e+03 pdb=" N1 5MU A2177 " 0.044 2.00e-02 2.50e+03 ... (remaining 12697 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2959 2.60 - 3.18: 105657 3.18 - 3.75: 293605 3.75 - 4.33: 420410 4.33 - 4.90: 549869 Nonbonded interactions: 1372500 Sorted by model distance: nonbonded pdb=" OP1 A A2014 " pdb="MG MG A3223 " model vdw 2.026 2.170 nonbonded pdb=" OP1 A A2959 " pdb="MG MG A3341 " model vdw 2.027 2.170 nonbonded pdb=" OP1 C a1295 " pdb="MG MG a1655 " model vdw 2.048 2.170 nonbonded pdb=" OP2 C A 619 " pdb="MG MG A3285 " model vdw 2.048 2.170 nonbonded pdb=" OP1 A A1073 " pdb="MG MG A3210 " model vdw 2.053 2.170 ... (remaining 1372495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'x' selection = (chain 'y' and ((resid 1 and (name P or name OP1 or name OP2 or name O5' or name \ C5' or name C4' or name O4' or name C3' or name O3' or name C2' or name O2' or \ name C1' or name N1 or name C2 or name O2 or name N3 or name C4 or name N4 or na \ me C5 or name C6 )) or resid 2 through 77)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 12.700 Check model and map are aligned: 1.600 Set scattering table: 1.010 Process input model: 630.260 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 663.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.292 162502 Z= 0.442 Angle : 0.860 23.260 243960 Z= 0.426 Chirality : 0.045 0.434 31239 Planarity : 0.011 0.576 12700 Dihedral : 22.807 179.902 94504 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.09), residues: 5526 helix: -4.23 (0.06), residues: 1659 sheet: -1.50 (0.15), residues: 1062 loop : -2.31 (0.10), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP Q 61 HIS 0.024 0.003 HIS o 51 PHE 0.048 0.004 PHE E 90 TYR 0.047 0.003 TYR E 104 ARG 0.019 0.002 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1072 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 150 SER cc_start: 0.7781 (t) cc_final: 0.7576 (t) REVERT: E 29 GLU cc_start: 0.7581 (pp20) cc_final: 0.7324 (pp20) REVERT: R 69 THR cc_start: 0.8456 (p) cc_final: 0.8226 (t) REVERT: Y 21 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8136 (mmm-85) REVERT: g 24 THR cc_start: 0.9083 (t) cc_final: 0.8833 (m) REVERT: l 93 VAL cc_start: 0.8509 (t) cc_final: 0.8283 (p) outliers start: 8 outliers final: 2 residues processed: 1078 average time/residue: 2.6931 time to fit residues: 3937.2458 Evaluate side-chains 709 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 707 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain r residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 867 optimal weight: 5.9990 chunk 778 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 525 optimal weight: 1.9990 chunk 415 optimal weight: 8.9990 chunk 804 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 489 optimal weight: 0.3980 chunk 599 optimal weight: 5.9990 chunk 932 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 28 ASN 1 49 GLN 7 17 ASN 8 172 HIS 8 231 ASN C 87 ASN C 113 GLN C 130 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN F 146 HIS G 62 ASN J 58 ASN J 147 GLN ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Q 94 ASN Q 122 ASN S 71 ASN V 91 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN c 111 GLN c 143 GLN c 176 HIS d 35 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN e 117 GLN e 163 ASN e 179 GLN g 122 ASN i 65 HIS k 111 GLN o 51 HIS p 15 ASN q 99 HIS r 56 ASN s 22 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 162502 Z= 0.313 Angle : 0.652 16.507 243960 Z= 0.337 Chirality : 0.040 0.285 31239 Planarity : 0.006 0.130 12700 Dihedral : 23.290 179.890 83569 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 3.12 % Allowed : 13.02 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 5526 helix: -1.95 (0.10), residues: 1688 sheet: -0.96 (0.15), residues: 1050 loop : -1.84 (0.10), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 22 HIS 0.013 0.002 HIS M 13 PHE 0.020 0.002 PHE T 31 TYR 0.022 0.002 TYR C 104 ARG 0.013 0.001 ARG g 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 720 time to evaluate : 6.163 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: 8 51 ASP cc_start: 0.7432 (t0) cc_final: 0.7006 (p0) REVERT: C 68 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7616 (mmt180) REVERT: D 185 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8214 (t) REVERT: E 29 GLU cc_start: 0.7654 (pp20) cc_final: 0.7406 (pp20) REVERT: J 75 TYR cc_start: 0.8534 (m-80) cc_final: 0.8324 (m-80) REVERT: M 128 LYS cc_start: 0.8479 (mttt) cc_final: 0.7938 (mttt) REVERT: P 93 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7656 (mmp80) REVERT: R 69 THR cc_start: 0.8796 (p) cc_final: 0.8562 (t) REVERT: T 77 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8425 (pttp) REVERT: U 5 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8189 (tttt) REVERT: V 99 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7884 (ptp90) REVERT: c 57 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6355 (pt0) REVERT: c 166 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6661 (mm-30) REVERT: f 1 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6563 (mmt) REVERT: g 78 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.5908 (tpt90) REVERT: i 140 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7860 (mptp) REVERT: l 60 GLN cc_start: 0.8239 (mm-40) cc_final: 0.8020 (mp-120) REVERT: m 79 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7354 (tpp80) REVERT: q 78 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7813 (pp20) REVERT: t 5 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8496 (tttm) outliers start: 143 outliers final: 49 residues processed: 794 average time/residue: 2.2835 time to fit residues: 2554.0427 Evaluate side-chains 729 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 670 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 5 LYS Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain i residue 140 LYS Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 518 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 776 optimal weight: 10.0000 chunk 635 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 934 optimal weight: 5.9990 chunk 1009 optimal weight: 10.0000 chunk 832 optimal weight: 9.9990 chunk 926 optimal weight: 0.0770 chunk 318 optimal weight: 7.9990 chunk 749 optimal weight: 10.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 28 ASN 3 28 ASN 8 168 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN M 13 HIS S 71 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN g 122 ASN i 52 ASN k 85 GLN o 7 GLN t 8 GLN t 71 GLN t 84 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 162502 Z= 0.368 Angle : 0.657 13.836 243960 Z= 0.338 Chirality : 0.040 0.274 31239 Planarity : 0.006 0.126 12700 Dihedral : 23.077 179.833 83565 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 4.04 % Allowed : 14.77 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 5526 helix: -0.78 (0.12), residues: 1685 sheet: -0.71 (0.15), residues: 1103 loop : -1.58 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 22 HIS 0.008 0.002 HIS M 13 PHE 0.018 0.002 PHE E 150 TYR 0.022 0.002 TYR C 104 ARG 0.012 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 744 time to evaluate : 5.981 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: 4 31 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8317 (ttp-170) REVERT: 4 33 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7460 (ttmt) REVERT: 8 51 ASP cc_start: 0.7517 (t0) cc_final: 0.7062 (p0) REVERT: 8 193 ILE cc_start: 0.7224 (mt) cc_final: 0.7011 (mm) REVERT: E 10 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8243 (tptt) REVERT: E 29 GLU cc_start: 0.7681 (pp20) cc_final: 0.7394 (pp20) REVERT: E 32 ASP cc_start: 0.7832 (t0) cc_final: 0.7534 (t0) REVERT: E 81 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7944 (ptt90) REVERT: J 75 TYR cc_start: 0.8524 (m-80) cc_final: 0.8324 (m-80) REVERT: M 16 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6875 (mtm-85) REVERT: M 82 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8278 (mpt-90) REVERT: N 117 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6375 (mtp85) REVERT: P 93 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7797 (mmp80) REVERT: R 69 THR cc_start: 0.8861 (p) cc_final: 0.8629 (t) REVERT: T 77 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8432 (pttp) REVERT: c 166 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6675 (mm-30) REVERT: d 131 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7944 (mtm180) REVERT: e 43 LEU cc_start: 0.8542 (mm) cc_final: 0.8329 (mt) REVERT: e 60 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7389 (mtm180) REVERT: f 1 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6776 (mmt) REVERT: g 78 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5570 (tpt90) REVERT: i 140 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7927 (mptp) REVERT: p 39 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7505 (ptm-80) REVERT: q 78 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7950 (pp20) REVERT: s 32 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8007 (ttmp) outliers start: 185 outliers final: 84 residues processed: 835 average time/residue: 2.3190 time to fit residues: 2731.5714 Evaluate side-chains 800 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 700 time to evaluate : 5.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 181 ASP Chi-restraints excluded: chain 8 residue 228 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 156 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain d residue 111 GLN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain i residue 140 LYS Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 120 SER Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 923 optimal weight: 4.9990 chunk 702 optimal weight: 10.0000 chunk 484 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 627 optimal weight: 10.0000 chunk 937 optimal weight: 0.9990 chunk 992 optimal weight: 6.9990 chunk 489 optimal weight: 4.9990 chunk 888 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN L 83 ASN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN h 93 ASN i 52 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 162502 Z= 0.234 Angle : 0.581 13.594 243960 Z= 0.304 Chirality : 0.036 0.254 31239 Planarity : 0.005 0.122 12700 Dihedral : 23.044 179.675 83565 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 3.56 % Allowed : 16.80 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5526 helix: -0.23 (0.13), residues: 1706 sheet: -0.57 (0.16), residues: 1088 loop : -1.40 (0.11), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 22 HIS 0.005 0.001 HIS F 146 PHE 0.014 0.001 PHE G 132 TYR 0.016 0.001 TYR C 104 ARG 0.014 0.001 ARG V 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 712 time to evaluate : 5.493 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: 4 31 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8301 (ttp-170) REVERT: 4 33 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7424 (ttmt) REVERT: 8 53 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7525 (mtm180) REVERT: 8 54 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: D 4 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: E 10 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8254 (tptt) REVERT: E 29 GLU cc_start: 0.7660 (pp20) cc_final: 0.7381 (pp20) REVERT: E 32 ASP cc_start: 0.7795 (t0) cc_final: 0.7485 (t0) REVERT: J 75 TYR cc_start: 0.8518 (m-80) cc_final: 0.8309 (m-80) REVERT: K 94 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7718 (ttp-170) REVERT: M 82 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8249 (mpt-90) REVERT: P 38 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.5940 (ptm160) REVERT: P 93 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7782 (mmp80) REVERT: T 77 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8419 (pttp) REVERT: X 21 SER cc_start: 0.8567 (p) cc_final: 0.8356 (t) REVERT: c 166 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6628 (mm-30) REVERT: d 179 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: f 1 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6814 (mmt) REVERT: g 78 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.5474 (tpt90) REVERT: h 96 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6892 (mtt90) REVERT: i 78 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7740 (mtp85) REVERT: i 134 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: m 79 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7544 (ttm-80) REVERT: m 115 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.6660 (mpp-170) REVERT: p 14 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6483 (mtp180) REVERT: p 39 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7501 (ptm-80) REVERT: q 78 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (pp20) outliers start: 163 outliers final: 84 residues processed: 793 average time/residue: 2.3141 time to fit residues: 2596.6654 Evaluate side-chains 783 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 681 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 156 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 190 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 134 ARG Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 826 optimal weight: 2.9990 chunk 563 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 739 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 847 optimal weight: 7.9990 chunk 686 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 506 optimal weight: 0.9990 chunk 891 optimal weight: 6.9990 chunk 250 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: 1 22 ASN 1 28 ASN D 34 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 162502 Z= 0.339 Angle : 0.626 13.728 243960 Z= 0.322 Chirality : 0.039 0.264 31239 Planarity : 0.005 0.125 12700 Dihedral : 22.986 179.174 83565 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 4.21 % Allowed : 17.15 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5526 helix: -0.02 (0.13), residues: 1717 sheet: -0.53 (0.15), residues: 1122 loop : -1.31 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 22 HIS 0.007 0.001 HIS C 231 PHE 0.016 0.002 PHE i 85 TYR 0.020 0.002 TYR n 34 ARG 0.010 0.001 ARG q 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 702 time to evaluate : 6.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 21 LYS cc_start: 0.8769 (pttt) cc_final: 0.8462 (pttt) REVERT: 4 31 ARG cc_start: 0.8582 (ptp-170) cc_final: 0.8294 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8564 (mttp) REVERT: 8 151 LYS cc_start: 0.7253 (tmmt) cc_final: 0.7038 (pptt) REVERT: 8 160 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.5736 (ptmt) REVERT: C 26 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7017 (ttm-80) REVERT: C 68 ARG cc_start: 0.7950 (mmt90) cc_final: 0.7641 (mmt180) REVERT: E 10 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8233 (tptt) REVERT: E 29 GLU cc_start: 0.7715 (pp20) cc_final: 0.7426 (pp20) REVERT: E 32 ASP cc_start: 0.7830 (t0) cc_final: 0.7570 (t0) REVERT: E 81 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7864 (ptt90) REVERT: F 25 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8459 (mmmt) REVERT: F 33 MET cc_start: 0.8672 (mmt) cc_final: 0.7961 (mmp) REVERT: F 90 MET cc_start: 0.7855 (mtp) cc_final: 0.7526 (mpp) REVERT: G 95 TYR cc_start: 0.8898 (m-80) cc_final: 0.8695 (m-80) REVERT: J 75 TYR cc_start: 0.8526 (m-80) cc_final: 0.8296 (m-80) REVERT: K 94 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7775 (ttp-170) REVERT: M 82 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7716 (mpt-90) REVERT: N 117 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6534 (mpp80) REVERT: P 38 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.5902 (ptm160) REVERT: P 93 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7835 (mmp80) REVERT: Q 73 ASP cc_start: 0.7198 (p0) cc_final: 0.6990 (p0) REVERT: T 77 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8426 (pttp) REVERT: d 38 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: d 131 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7938 (mtm180) REVERT: d 179 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: e 60 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7585 (mtm180) REVERT: g 24 THR cc_start: 0.9024 (t) cc_final: 0.8792 (m) REVERT: g 78 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5624 (tpt90) REVERT: g 143 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8282 (mtmt) REVERT: h 96 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6921 (mtt90) REVERT: i 78 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7774 (mtp85) REVERT: i 140 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7886 (mptp) REVERT: m 79 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7631 (ttm-80) REVERT: m 115 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6534 (mpp-170) REVERT: p 14 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6526 (mtp180) REVERT: p 39 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7493 (ptm-80) REVERT: q 78 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7991 (pp20) outliers start: 193 outliers final: 109 residues processed: 800 average time/residue: 2.3104 time to fit residues: 2641.3969 Evaluate side-chains 827 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 695 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 49 LEU Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 120 ARG Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 156 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 30 GLU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 190 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 38 ARG Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 134 ARG Chi-restraints excluded: chain i residue 140 LYS Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 333 optimal weight: 6.9990 chunk 893 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 582 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 993 optimal weight: 10.0000 chunk 824 optimal weight: 8.9990 chunk 460 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 328 optimal weight: 8.9990 chunk 521 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN L 83 ASN M 96 ASN O 48 ASN Q 44 ASN U 62 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 162502 Z= 0.434 Angle : 0.686 13.785 243960 Z= 0.348 Chirality : 0.042 0.292 31239 Planarity : 0.006 0.126 12700 Dihedral : 22.972 178.525 83565 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 4.65 % Allowed : 17.26 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5526 helix: 0.04 (0.13), residues: 1708 sheet: -0.46 (0.16), residues: 1110 loop : -1.29 (0.11), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 8 108 HIS 0.008 0.002 HIS N 54 PHE 0.017 0.002 PHE 6 22 TYR 0.025 0.002 TYR n 34 ARG 0.012 0.001 ARG q 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 705 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 21 LYS cc_start: 0.8775 (pttt) cc_final: 0.8488 (pttt) REVERT: 4 31 ARG cc_start: 0.8606 (ptp-170) cc_final: 0.8333 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8513 (mttp) REVERT: 8 160 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.5775 (ptmt) REVERT: 8 167 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8829 (mptm) REVERT: C 26 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7665 (tmm-80) REVERT: C 68 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7650 (mmt180) REVERT: D 133 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7157 (mtt-85) REVERT: E 29 GLU cc_start: 0.7788 (pp20) cc_final: 0.7457 (pp20) REVERT: E 32 ASP cc_start: 0.7851 (t0) cc_final: 0.7610 (t0) REVERT: E 81 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7924 (ptt90) REVERT: F 25 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: F 90 MET cc_start: 0.7792 (mtp) cc_final: 0.7285 (mpp) REVERT: J 75 TYR cc_start: 0.8535 (m-80) cc_final: 0.8333 (m-80) REVERT: K 94 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: M 82 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7957 (mpt-90) REVERT: N 117 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6643 (mpp80) REVERT: P 38 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6057 (ptm160) REVERT: P 93 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7828 (mmp80) REVERT: Q 73 ASP cc_start: 0.7220 (p0) cc_final: 0.7007 (p0) REVERT: S 37 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6800 (mmm160) REVERT: S 41 ASP cc_start: 0.6797 (t0) cc_final: 0.6549 (m-30) REVERT: T 77 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8434 (pttp) REVERT: U 96 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7738 (ttp-170) REVERT: c 204 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8013 (mtpt) REVERT: d 38 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7523 (mtp180) REVERT: d 48 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8540 (tp) REVERT: d 126 ASN cc_start: 0.9064 (p0) cc_final: 0.8796 (p0) REVERT: d 131 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7957 (mtm180) REVERT: d 179 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: e 45 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7879 (mtt-85) REVERT: e 60 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7644 (mtm180) REVERT: f 1 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7011 (mmt) REVERT: g 24 THR cc_start: 0.9059 (t) cc_final: 0.8837 (m) REVERT: g 78 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.5541 (tpt90) REVERT: g 143 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8265 (mtmt) REVERT: h 96 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7017 (mtt90) REVERT: i 78 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7755 (mtp85) REVERT: i 140 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7925 (mptp) REVERT: m 79 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7707 (ttm-80) REVERT: m 115 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6562 (mpp-170) REVERT: n 19 ARG cc_start: 0.9156 (ttm170) cc_final: 0.8889 (mtt180) REVERT: p 14 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.6603 (mtp180) REVERT: p 29 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8409 (ttp-170) REVERT: p 39 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7331 (ptm-80) REVERT: q 78 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7976 (pp20) outliers start: 213 outliers final: 125 residues processed: 812 average time/residue: 2.2597 time to fit residues: 2611.2646 Evaluate side-chains 849 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 693 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 49 LEU Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain 8 residue 167 LYS Chi-restraints excluded: chain 8 residue 228 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 8 LYS Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 96 ARG Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 30 GLU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 190 LYS Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 38 ARG Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 61 ARG Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 143 LYS Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 134 ARG Chi-restraints excluded: chain i residue 140 LYS Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 29 ARG Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 958 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 566 optimal weight: 2.9990 chunk 725 optimal weight: 8.9990 chunk 562 optimal weight: 1.9990 chunk 836 optimal weight: 0.0370 chunk 554 optimal weight: 1.9990 chunk 989 optimal weight: 6.9990 chunk 619 optimal weight: 0.9990 chunk 603 optimal weight: 0.9990 chunk 457 optimal weight: 1.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN 8 170 ASN E 159 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN O 48 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 ASN c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.112 162502 Z= 0.141 Angle : 0.581 15.639 243960 Z= 0.305 Chirality : 0.035 0.413 31239 Planarity : 0.005 0.120 12700 Dihedral : 23.087 178.581 83565 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 3.16 % Allowed : 19.76 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5526 helix: 0.38 (0.13), residues: 1713 sheet: -0.31 (0.16), residues: 1052 loop : -1.16 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 8 108 HIS 0.005 0.001 HIS F 146 PHE 0.014 0.001 PHE i 85 TYR 0.015 0.001 TYR c 184 ARG 0.010 0.001 ARG 8 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 708 time to evaluate : 6.106 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: 4 31 ARG cc_start: 0.8513 (ptp-170) cc_final: 0.8298 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (mttp) REVERT: 8 160 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.5825 (ptmt) REVERT: C 26 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6945 (ttm-80) REVERT: C 68 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7588 (mmt180) REVERT: D 133 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7037 (mtt-85) REVERT: E 10 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (tptt) REVERT: E 29 GLU cc_start: 0.7761 (pp20) cc_final: 0.7472 (pp20) REVERT: E 81 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7626 (ptt90) REVERT: F 25 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8465 (mmmt) REVERT: F 90 MET cc_start: 0.7744 (mtp) cc_final: 0.7395 (mpp) REVERT: M 82 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8243 (mpt-90) REVERT: N 114 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: P 38 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6014 (ptm160) REVERT: P 93 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7694 (mmp80) REVERT: S 37 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6699 (mmm160) REVERT: d 131 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7903 (mtm180) REVERT: d 179 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: e 45 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7778 (mtt-85) REVERT: g 24 THR cc_start: 0.8996 (t) cc_final: 0.8766 (m) REVERT: g 78 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5423 (tpt90) REVERT: g 143 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8266 (mtmt) REVERT: h 96 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6971 (mtt90) REVERT: i 78 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7709 (mtp85) REVERT: l 110 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8371 (tpt-90) REVERT: m 79 ARG cc_start: 0.7952 (tpp80) cc_final: 0.7664 (ttm-80) REVERT: m 115 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6486 (mpp-170) REVERT: p 14 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6473 (mtp180) REVERT: p 29 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8327 (ttp-170) REVERT: p 94 LYS cc_start: 0.8765 (pttp) cc_final: 0.8419 (pttm) REVERT: q 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7893 (pp20) outliers start: 145 outliers final: 88 residues processed: 785 average time/residue: 2.3098 time to fit residues: 2592.0707 Evaluate side-chains 794 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 685 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 30 GLU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 190 LYS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 29 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 612 optimal weight: 0.8980 chunk 395 optimal weight: 6.9990 chunk 591 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 629 optimal weight: 0.4980 chunk 674 optimal weight: 10.0000 chunk 489 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 778 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN 8 170 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN M 96 ASN O 48 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN g 122 ASN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 162502 Z= 0.287 Angle : 0.599 13.628 243960 Z= 0.310 Chirality : 0.037 0.306 31239 Planarity : 0.005 0.124 12700 Dihedral : 22.951 178.255 83565 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.32 % Allowed : 20.03 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 5526 helix: 0.44 (0.13), residues: 1723 sheet: -0.31 (0.16), residues: 1100 loop : -1.15 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 8 108 HIS 0.006 0.001 HIS C 231 PHE 0.015 0.002 PHE i 85 TYR 0.022 0.002 TYR r 32 ARG 0.014 0.001 ARG q 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 682 time to evaluate : 6.122 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: 4 31 ARG cc_start: 0.8582 (ptp-170) cc_final: 0.8327 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: 8 160 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.5804 (ptmt) REVERT: C 26 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7466 (tmm-80) REVERT: C 68 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7633 (mmt180) REVERT: D 133 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7110 (mtt-85) REVERT: D 207 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7273 (ttp) REVERT: E 10 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (tptt) REVERT: E 29 GLU cc_start: 0.7763 (pp20) cc_final: 0.7472 (pp20) REVERT: E 81 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7838 (ptt90) REVERT: F 90 MET cc_start: 0.7762 (mtp) cc_final: 0.7405 (mpp) REVERT: M 82 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8081 (mpt-90) REVERT: N 117 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6329 (mtp85) REVERT: P 38 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.5961 (ptm160) REVERT: P 93 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7787 (mmp80) REVERT: S 37 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6823 (mmm160) REVERT: T 77 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8394 (pttp) REVERT: d 131 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: d 179 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: f 1 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.6962 (mmt) REVERT: g 24 THR cc_start: 0.9012 (t) cc_final: 0.8803 (m) REVERT: g 78 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.5590 (tpt90) REVERT: g 143 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8269 (mtmt) REVERT: h 96 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7009 (mtt90) REVERT: i 78 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7692 (mtp85) REVERT: i 134 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8430 (ptm-80) REVERT: l 110 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8425 (tpt-90) REVERT: m 79 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7691 (ttm-80) REVERT: m 115 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6480 (mpp-170) REVERT: p 14 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6535 (mtp180) REVERT: p 29 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8359 (ttp-170) REVERT: q 78 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7953 (pp20) outliers start: 152 outliers final: 98 residues processed: 760 average time/residue: 2.3176 time to fit residues: 2505.4360 Evaluate side-chains 806 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 684 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 49 LEU Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 134 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 111 LYS Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 29 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 900 optimal weight: 9.9990 chunk 948 optimal weight: 10.0000 chunk 865 optimal weight: 3.9990 chunk 922 optimal weight: 9.9990 chunk 555 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 724 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 833 optimal weight: 5.9990 chunk 872 optimal weight: 3.9990 chunk 919 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN 8 170 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN O 48 ASN U 62 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 162502 Z= 0.406 Angle : 0.665 13.737 243960 Z= 0.339 Chirality : 0.041 0.349 31239 Planarity : 0.006 0.126 12700 Dihedral : 22.938 177.877 83565 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 3.49 % Allowed : 19.98 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5526 helix: 0.35 (0.13), residues: 1718 sheet: -0.32 (0.16), residues: 1077 loop : -1.20 (0.12), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP h 132 HIS 0.008 0.001 HIS L 126 PHE 0.017 0.002 PHE 6 22 TYR 0.024 0.002 TYR 8 21 ARG 0.015 0.001 ARG q 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 691 time to evaluate : 6.093 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: 4 31 ARG cc_start: 0.8589 (ptp-170) cc_final: 0.8332 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8477 (mttp) REVERT: 8 160 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5927 (ptmt) REVERT: C 26 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7593 (tmm-80) REVERT: D 133 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7132 (mtt-85) REVERT: E 29 GLU cc_start: 0.7809 (pp20) cc_final: 0.7484 (pp20) REVERT: E 81 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7835 (ptt90) REVERT: M 82 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7991 (mpt-90) REVERT: M 124 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7903 (mptt) REVERT: N 117 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6427 (mtp85) REVERT: P 38 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.5960 (ptm160) REVERT: P 93 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7814 (mmp80) REVERT: S 37 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6775 (mmm160) REVERT: S 41 ASP cc_start: 0.6790 (t0) cc_final: 0.6550 (m-30) REVERT: T 77 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8394 (pttp) REVERT: d 48 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8522 (tp) REVERT: d 131 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7953 (mtm180) REVERT: d 179 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: e 60 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7156 (mtm-85) REVERT: f 1 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: g 78 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.5565 (tpt90) REVERT: g 143 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8286 (mtmt) REVERT: h 96 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7044 (mtt90) REVERT: i 78 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7674 (mtp85) REVERT: i 134 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8490 (ptm-80) REVERT: m 79 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7771 (ttm-80) REVERT: m 115 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6482 (mpp-170) REVERT: p 14 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.6587 (mtp180) REVERT: p 29 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8322 (ttp-170) REVERT: q 78 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7950 (pp20) outliers start: 160 outliers final: 108 residues processed: 771 average time/residue: 2.3449 time to fit residues: 2589.2799 Evaluate side-chains 815 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 683 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 49 LEU Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 124 LYS Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 156 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 134 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 111 LYS Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 29 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 605 optimal weight: 0.8980 chunk 975 optimal weight: 2.9990 chunk 595 optimal weight: 0.9980 chunk 462 optimal weight: 0.2980 chunk 678 optimal weight: 10.0000 chunk 1023 optimal weight: 8.9990 chunk 941 optimal weight: 10.0000 chunk 814 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 629 optimal weight: 8.9990 chunk 499 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN O 48 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 162502 Z= 0.141 Angle : 0.580 13.802 243960 Z= 0.303 Chirality : 0.034 0.345 31239 Planarity : 0.005 0.119 12700 Dihedral : 23.045 178.208 83565 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 2.64 % Allowed : 20.90 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 5526 helix: 0.58 (0.13), residues: 1725 sheet: -0.24 (0.16), residues: 1060 loop : -1.08 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.005 0.001 HIS F 146 PHE 0.015 0.001 PHE i 85 TYR 0.018 0.001 TYR Q 47 ARG 0.031 0.001 ARG m 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 689 time to evaluate : 5.449 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: 0 41 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7942 (ttt180) REVERT: 4 31 ARG cc_start: 0.8516 (ptp-170) cc_final: 0.8292 (ttp-170) REVERT: 8 54 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: 8 160 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5916 (ptmt) REVERT: C 26 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6817 (ttm-80) REVERT: C 68 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7607 (mmt180) REVERT: C 226 MET cc_start: 0.8008 (mtt) cc_final: 0.7802 (mtt) REVERT: D 133 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7065 (mtt-85) REVERT: D 207 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7280 (ttp) REVERT: E 10 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8280 (tptt) REVERT: E 29 GLU cc_start: 0.7785 (pp20) cc_final: 0.7489 (pp20) REVERT: E 81 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7648 (ptt90) REVERT: F 90 MET cc_start: 0.7801 (mtp) cc_final: 0.7387 (mpp) REVERT: M 82 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8285 (mpt-90) REVERT: N 117 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6269 (mtp85) REVERT: P 38 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.6020 (ptm160) REVERT: P 93 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7717 (mmp80) REVERT: S 37 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6686 (mmm160) REVERT: W 14 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7637 (ptt90) REVERT: d 131 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7913 (mtm180) REVERT: d 179 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: f 1 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: g 78 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.5437 (tpt90) REVERT: g 143 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8263 (mtmt) REVERT: h 96 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7015 (mtt90) REVERT: i 78 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7632 (mtp85) REVERT: l 110 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8356 (tpt-90) REVERT: m 79 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7746 (ttm-80) REVERT: m 115 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6411 (mpp-170) REVERT: p 29 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8232 (ttp-170) REVERT: p 94 LYS cc_start: 0.8773 (pttp) cc_final: 0.8436 (pttm) REVERT: q 78 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7881 (pp20) outliers start: 121 outliers final: 80 residues processed: 752 average time/residue: 2.2795 time to fit residues: 2437.3225 Evaluate side-chains 783 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 679 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 41 ARG Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 72 THR Chi-restraints excluded: chain 8 residue 160 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 146 ILE Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 111 LYS Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 115 ARG Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain p residue 29 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 GLU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1027 random chunks: chunk 647 optimal weight: 0.4980 chunk 867 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 751 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 816 optimal weight: 30.0000 chunk 341 optimal weight: 10.0000 chunk 837 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 8 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN O 48 ASN U 62 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN l 109 ASN o 7 GLN t 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.073500 restraints weight = 220282.213| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 0.94 r_work: 0.2715 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 162502 Z= 0.467 Angle : 0.693 13.814 243960 Z= 0.350 Chirality : 0.043 0.361 31239 Planarity : 0.006 0.127 12700 Dihedral : 22.918 177.788 83565 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 2.73 % Allowed : 21.07 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5526 helix: 0.39 (0.13), residues: 1718 sheet: -0.32 (0.16), residues: 1101 loop : -1.17 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 132 HIS 0.009 0.002 HIS C 231 PHE 0.018 0.002 PHE E 202 TYR 0.020 0.002 TYR Q 47 ARG 0.016 0.001 ARG q 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41788.18 seconds wall clock time: 728 minutes 2.11 seconds (43682.11 seconds total)