Starting phenix.real_space_refine on Wed Jan 17 21:45:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk0_17719/01_2024/8pk0_17719_neut_updated.pdb" } resolution = 3.03 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= -0.004 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 10 8.98 5 Zn 1 6.06 5 P 1502 5.49 5 Mg 96 5.21 5 S 318 5.16 5 C 63004 2.51 5 N 19730 2.21 5 O 24041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 159": "OD1" <-> "OD2" Residue "x PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 108702 Number of models: 1 Model: "" Number of chains: 66 Chain: "0" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "T" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1369 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "u" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1044 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "1" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "U" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1251 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "V" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1676 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 186} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "3" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 832 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "W" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 835 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "x" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2676 Classifications: {'peptide': 338} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "5" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3210 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 361} Chain: "X" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2044 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "y" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1980 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "6" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2948 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 319} Chain: "Y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1556 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "z" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2443 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 297} Chain: "7" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2390 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain: "Z" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "8" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 10, 'TRANS': 91} Chain: "a" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 840 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 88} Chain breaks: 1 Chain: "9" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 113} Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1189 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 9, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'THC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 30199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 30199 Classifications: {'RNA': 1423} Modifications used: {'rna2p_pur': 146, 'rna2p_pyr': 116, 'rna3p_pur': 602, 'rna3p_pyr': 559} Link IDs: {'rna2p': 261, 'rna3p': 1161} Chain breaks: 13 Chain: "c" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2299 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 268} Chain breaks: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1522 Classifications: {'RNA': 72} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 8, 'rna3p': 63} Chain: "d" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2088 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 20, 'TRANS': 234} Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain: "e" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1848 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "E" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2406 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 280} Chain: "f" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1196 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2031 Classifications: {'peptide': 252} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 230} Chain: "g" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1113 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 117} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "h" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 895 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "I" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 871 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 15, 'TRANS': 142} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "i" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 828 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 798 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 151} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 570 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "j" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 7, 'TRANS': 82} Chain: "K" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1455 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 502 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'AYA:plan-2': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 157 Chain: "L" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "l" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 353 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2327 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 264} Chain: "m" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 419 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 799 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 213 Chain: "o" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 677 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1259 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "p" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 2 Chain: "P" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1173 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 136} Chain: "q" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1177 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 14, 'TRANS': 126} Chain: "Q" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1843 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Chain: "r" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1251 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 142} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "s" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3155 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 358} Chain breaks: 1 Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1293 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain: "t" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1958 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 13, 'TRANS': 311} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 485 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 292 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PM8': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Unusual residues: {' K': 10, ' MG': 92} Classifications: {'undetermined': 102} Link IDs: {None: 101} 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: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 74.454 161.702 69.672 1.00 54.80 S ATOM 286 SG CYS 0 113 73.186 158.451 68.239 1.00 55.45 S ATOM 366 SG CYS 0 123 76.305 158.488 70.358 1.00 52.64 S ATOM 389 SG CYS 0 126 76.358 159.994 66.900 1.00 58.83 S Time building chain proxies: 39.71, per 1000 atoms: 0.37 Number of scatterers: 108702 At special positions: 0 Unit cell: (209.52, 237.6, 262.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 10 19.00 S 318 16.00 P 1502 15.00 Mg 96 11.99 O 24041 8.00 N 19730 7.00 C 63004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS r 70 " - pdb=" SG CYS r 73 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.73 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 201 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 113 " Number of angles added : 6 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18332 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: 335 helices and 80 sheets defined 43.4% alpha, 13.5% beta 360 base pairs and 744 stacking pairs defined. Time for finding SS restraints: 65.91 Creating SS restraints... Processing helix chain '0' and resid 86 through 96 removed outlier: 4.049A pdb=" N ASN 0 96 " --> pdb=" O CYS 0 92 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 Processing helix chain 'T' and resid 43 through 51 removed outlier: 3.869A pdb=" N LYS T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN T 49 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE T 51 " --> pdb=" O LYS T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 89 removed outlier: 3.906A pdb=" N TYR T 83 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.554A pdb=" N PHE T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 125 removed outlier: 4.362A pdb=" N LYS T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.836A pdb=" N ARG T 200 " --> pdb=" O GLN T 196 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 removed outlier: 3.589A pdb=" N GLN u 103 " --> pdb=" O SER u 99 " (cutoff:3.500A) Processing helix chain 'u' and resid 131 through 150 removed outlier: 3.987A pdb=" N LYS u 150 " --> pdb=" O TYR u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 Processing helix chain 'u' and resid 190 through 196 Processing helix chain 'u' and resid 200 through 207 removed outlier: 4.868A pdb=" N ALA u 207 " --> pdb=" O LEU u 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 112 through 118 Proline residue: U 118 - end of helix Processing helix chain 'U' and resid 124 through 137 Processing helix chain 'v' and resid 5 through 23 Processing helix chain 'v' and resid 27 through 43 Processing helix chain 'v' and resid 47 through 64 removed outlier: 6.270A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 73 removed outlier: 4.214A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Proline residue: 2 73 - end of helix Processing helix chain '2' and resid 74 through 86 Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 50 through 55 removed outlier: 5.921A pdb=" N TYR V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 121 removed outlier: 4.963A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.736A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 4.561A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 5.455A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 Processing helix chain 'w' and resid 103 through 109 removed outlier: 3.577A pdb=" N LEU w 108 " --> pdb=" O HIS w 103 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.795A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.156A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 4.065A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.161A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 removed outlier: 3.605A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 57 removed outlier: 4.744A pdb=" N VAL x 54 " --> pdb=" O MET x 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY x 57 " --> pdb=" O SER x 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 59 through 70 removed outlier: 4.733A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 Processing helix chain 'x' and resid 97 through 109 removed outlier: 4.391A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 170 removed outlier: 4.008A pdb=" N LEU x 163 " --> pdb=" O ASP x 159 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU x 164 " --> pdb=" O ALA x 160 " (cutoff:3.500A) Proline residue: x 165 - end of helix removed outlier: 3.921A pdb=" N GLY x 170 " --> pdb=" O VAL x 166 " (cutoff:3.500A) Processing helix chain 'x' and resid 185 through 195 removed outlier: 3.854A pdb=" N ALA x 190 " --> pdb=" O GLY x 186 " (cutoff:3.500A) Processing helix chain 'x' and resid 206 through 221 Processing helix chain 'x' and resid 222 through 228 removed outlier: 3.764A pdb=" N ARG x 226 " --> pdb=" O PRO x 222 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY x 228 " --> pdb=" O GLU x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 237 through 245 removed outlier: 4.520A pdb=" N TRP x 241 " --> pdb=" O ASP x 237 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY x 242 " --> pdb=" O GLY x 238 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU x 243 " --> pdb=" O ARG x 239 " (cutoff:3.500A) Processing helix chain 'x' and resid 260 through 267 removed outlier: 3.657A pdb=" N HIS x 266 " --> pdb=" O ARG x 262 " (cutoff:3.500A) Processing helix chain 'x' and resid 277 through 300 Proline residue: x 285 - end of helix removed outlier: 5.397A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 4.310A pdb=" N TYR x 319 " --> pdb=" O LEU x 315 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL x 321 " --> pdb=" O ASN x 317 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 350 removed outlier: 3.549A pdb=" N VAL x 347 " --> pdb=" O HIS x 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE x 348 " --> pdb=" O PHE x 344 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP x 350 " --> pdb=" O ARG x 346 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 4.918A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.498A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 47 through 53' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.006A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 3.655A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 197 through 202 removed outlier: 4.697A pdb=" N ARG 5 201 " --> pdb=" O SER 5 197 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE 5 202 " --> pdb=" O LEU 5 198 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 197 through 202' Processing helix chain '5' and resid 241 through 252 removed outlier: 3.636A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.004A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.302A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.924A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.271A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 Processing helix chain 'X' and resid 197 through 205 removed outlier: 4.940A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY X 205 " --> pdb=" O ALA X 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 245 removed outlier: 3.854A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 103 Processing helix chain 'y' and resid 105 through 117 removed outlier: 5.388A pdb=" N ARG y 117 " --> pdb=" O LEU y 113 " (cutoff:3.500A) Processing helix chain 'y' and resid 120 through 135 Processing helix chain 'y' and resid 137 through 149 Proline residue: y 149 - end of helix Processing helix chain 'y' and resid 155 through 170 Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.357A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG y 178 " --> pdb=" O GLY y 174 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL y 179 " --> pdb=" O LYS y 175 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 203 removed outlier: 4.001A pdb=" N ILE y 194 " --> pdb=" O ARG y 190 " (cutoff:3.500A) Processing helix chain 'y' and resid 208 through 219 Processing helix chain 'y' and resid 220 through 226 removed outlier: 4.323A pdb=" N ARG y 224 " --> pdb=" O PRO y 220 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 240 Processing helix chain 'y' and resid 244 through 252 Processing helix chain 'y' and resid 257 through 272 Processing helix chain 'y' and resid 289 through 295 Processing helix chain 'y' and resid 297 through 305 Processing helix chain 'y' and resid 309 through 331 Processing helix chain '6' and resid 44 through 49 removed outlier: 5.288A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.705A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 6 67 " --> pdb=" O GLN 6 63 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 3.684A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 117 removed outlier: 5.541A pdb=" N VAL 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.637A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 removed outlier: 4.081A pdb=" N PHE 6 303 " --> pdb=" O ARG 6 299 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.069A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.688A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.814A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.956A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.561A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.382A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.534A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 5.371A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 239 removed outlier: 4.742A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'z' and resid 32 through 50 removed outlier: 3.851A pdb=" N GLY z 38 " --> pdb=" O HIS z 34 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS z 47 " --> pdb=" O GLN z 43 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU z 48 " --> pdb=" O SER z 44 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL z 49 " --> pdb=" O SER z 45 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP z 50 " --> pdb=" O LEU z 46 " (cutoff:3.500A) Processing helix chain 'z' and resid 67 through 72 removed outlier: 4.066A pdb=" N GLU z 71 " --> pdb=" O PRO z 67 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR z 72 " --> pdb=" O LEU z 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 67 through 72' Processing helix chain 'z' and resid 84 through 89 removed outlier: 3.632A pdb=" N ALA z 88 " --> pdb=" O LYS z 84 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP z 89 " --> pdb=" O MET z 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 84 through 89' Processing helix chain 'z' and resid 92 through 104 Processing helix chain 'z' and resid 118 through 134 removed outlier: 4.146A pdb=" N ILE z 122 " --> pdb=" O ASN z 118 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE z 123 " --> pdb=" O VAL z 119 " (cutoff:3.500A) Proline residue: z 124 - end of helix removed outlier: 3.752A pdb=" N SER z 133 " --> pdb=" O LEU z 129 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS z 134 " --> pdb=" O ILE z 130 " (cutoff:3.500A) Processing helix chain 'z' and resid 155 through 167 Processing helix chain 'z' and resid 213 through 224 Processing helix chain 'z' and resid 227 through 232 removed outlier: 3.943A pdb=" N VAL z 231 " --> pdb=" O LEU z 227 " (cutoff:3.500A) Processing helix chain 'z' and resid 233 through 248 Processing helix chain 'z' and resid 250 through 257 removed outlier: 4.255A pdb=" N GLN z 254 " --> pdb=" O PHE z 250 " (cutoff:3.500A) Processing helix chain 'z' and resid 264 through 277 Processing helix chain 'z' and resid 297 through 312 Processing helix chain 'z' and resid 320 through 326 Processing helix chain '7' and resid 36 through 60 removed outlier: 4.167A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.618A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE 7 154 " --> pdb=" O MET 7 150 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU 7 155 " --> pdb=" O GLY 7 151 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 4.146A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.558A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 47 removed outlier: 4.674A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 47' Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.751A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain '8' and resid 96 through 101 removed outlier: 4.615A pdb=" N GLU 8 100 " --> pdb=" O ASP 8 96 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG 8 101 " --> pdb=" O LYS 8 97 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 96 through 101' Processing helix chain '8' and resid 107 through 154 removed outlier: 3.798A pdb=" N LEU 8 123 " --> pdb=" O LYS 8 119 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 5.734A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 127 through 135 removed outlier: 6.262A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 53 through 58 removed outlier: 3.667A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 107 Processing helix chain '9' and resid 113 through 118 Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.618A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 49 removed outlier: 4.084A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 5.588A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 137 removed outlier: 4.647A pdb=" N ASN b 135 " --> pdb=" O HIS b 131 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS b 136 " --> pdb=" O PRO b 132 " (cutoff:3.500A) Proline residue: b 137 - end of helix No H-bonds generated for 'chain 'b' and resid 131 through 137' Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.274A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.656A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 4.057A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.654A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 109 Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.633A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.597A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.506A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 48 through 54 removed outlier: 4.570A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.540A pdb=" N SER d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 116 removed outlier: 5.236A pdb=" N MET d 116 " --> pdb=" O MET d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 117 through 130 Processing helix chain 'd' and resid 133 through 155 removed outlier: 4.058A pdb=" N PHE d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix removed outlier: 3.660A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 4.244A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU d 163 " --> pdb=" O ARG d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 5.400A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.843A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.705A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.535A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 101 Processing helix chain 'e' and resid 116 through 132 removed outlier: 4.952A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 Processing helix chain 'e' and resid 183 through 196 removed outlier: 5.720A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 4.412A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 265 through 276 removed outlier: 3.987A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.877A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.576A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.487A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.584A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.906A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.980A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 164 through 178 removed outlier: 3.768A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 189 through 194 removed outlier: 4.946A pdb=" N ASP f 193 " --> pdb=" O HIS f 189 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE f 194 " --> pdb=" O THR f 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 189 through 194' Processing helix chain 'f' and resid 200 through 212 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 109 removed outlier: 4.782A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.585A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.594A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.111A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 4.939A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.905A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 52 removed outlier: 4.310A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 133 removed outlier: 3.650A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.710A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 4.243A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 122 removed outlier: 4.074A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 149 Processing helix chain 'h' and resid 65 through 79 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.740A pdb=" N ILE h 89 " --> pdb=" O ASN h 85 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER h 90 " --> pdb=" O TRP h 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 85 through 90' Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.508A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.807A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.147A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.944A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.641A pdb=" N ARG I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU I 81 " --> pdb=" O GLY I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.623A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix removed outlier: 4.042A pdb=" N ASP I 137 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.850A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 148' Processing helix chain 'I' and resid 160 through 172 removed outlier: 4.119A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 3.993A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'J' and resid 33 through 43 removed outlier: 7.577A pdb=" N GLN J 37 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE J 38 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE J 42 " --> pdb=" O PHE J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 Proline residue: J 54 - end of helix Processing helix chain 'J' and resid 86 through 96 Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.700A pdb=" N ASP J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Proline residue: J 125 - end of helix Processing helix chain 'J' and resid 127 through 134 Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.658A pdb=" N LEU J 140 " --> pdb=" O SER J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 179 removed outlier: 4.193A pdb=" N ALA J 166 " --> pdb=" O ILE J 162 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 32 Processing helix chain 'j' and resid 60 through 105 removed outlier: 3.731A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG j 103 " --> pdb=" O GLN j 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.259A pdb=" N LEU j 46 " --> pdb=" O GLY j 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 41 through 46' Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.882A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG K 38 " --> pdb=" O MET K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.851A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.577A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 Proline residue: K 167 - end of helix Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'k' and resid 27 through 39 Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.730A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 102 Processing helix chain 'L' and resid 44 through 49 removed outlier: 5.379A pdb=" N SER L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 removed outlier: 4.289A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'l' and resid 65 through 71 Processing helix chain 'l' and resid 72 through 77 removed outlier: 4.472A pdb=" N TRP l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA l 77 " --> pdb=" O THR l 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 72 through 77' Processing helix chain 'l' and resid 88 through 93 removed outlier: 3.736A pdb=" N ARG l 92 " --> pdb=" O ALA l 88 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU l 93 " --> pdb=" O THR l 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 88 through 93' Processing helix chain 'l' and resid 94 through 99 removed outlier: 3.822A pdb=" N TYR l 98 " --> pdb=" O LEU l 94 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA l 99 " --> pdb=" O ALA l 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 94 through 99' Processing helix chain 'l' and resid 106 through 111 removed outlier: 4.898A pdb=" N LYS l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.586A pdb=" N ALA l 118 " --> pdb=" O VAL l 114 " (cutoff:3.500A) Proline residue: l 122 - end of helix Proline residue: l 128 - end of helix removed outlier: 4.012A pdb=" N ALA l 135 " --> pdb=" O LEU l 131 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 removed outlier: 4.628A pdb=" N ALA M 10 " --> pdb=" O GLN M 6 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 79 Proline residue: M 79 - end of helix Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.770A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.800A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.836A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix removed outlier: 3.562A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.808A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.222A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.698A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 removed outlier: 4.297A pdb=" N LYS N 197 " --> pdb=" O GLY N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.729A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU N 230 " --> pdb=" O ILE N 226 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 225 through 231' Processing helix chain 'N' and resid 232 through 237 removed outlier: 5.091A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 51 removed outlier: 3.848A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 4.315A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.442A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.385A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 5.104A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.432A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 4.036A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 162 Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 73 through 78 removed outlier: 3.956A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 73 through 78' Processing helix chain 'p' and resid 112 through 124 removed outlier: 3.674A pdb=" N LYS p 124 " --> pdb=" O ALA p 120 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 164 Processing helix chain 'p' and resid 172 through 190 removed outlier: 3.953A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.749A pdb=" N THR p 57 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA p 58 " --> pdb=" O SER p 55 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TRP p 59 " --> pdb=" O ASP p 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'P' and resid 39 through 44 removed outlier: 5.860A pdb=" N VAL P 44 " --> pdb=" O GLU P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 116 removed outlier: 4.655A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 156 removed outlier: 5.558A pdb=" N ASP P 156 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.340A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.541A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'q' and resid 78 through 93 removed outlier: 3.679A pdb=" N ARG q 83 " --> pdb=" O PRO q 79 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 165 removed outlier: 3.704A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.223A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 107 removed outlier: 3.901A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.746A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.053A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.734A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 261 removed outlier: 3.766A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 262 through 268 removed outlier: 4.062A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.696A pdb=" N ALA Q 280 " --> pdb=" O SER Q 276 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.133A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 Processing helix chain 'r' and resid 178 through 183 removed outlier: 3.940A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 'R' and resid 16 through 29 removed outlier: 4.559A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.702A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 80 removed outlier: 4.256A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 removed outlier: 4.782A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 73 Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.810A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 155 removed outlier: 3.988A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS s 154 " --> pdb=" O LEU s 150 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 193 removed outlier: 4.347A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER s 173 " --> pdb=" O SER s 169 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 307 through 315 Processing helix chain 's' and resid 318 through 344 removed outlier: 4.222A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 removed outlier: 3.640A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 4.266A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 90 removed outlier: 3.667A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.748A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 't' and resid 54 through 63 Proline residue: t 63 - end of helix Processing helix chain 't' and resid 160 through 170 removed outlier: 5.048A pdb=" N HIS t 170 " --> pdb=" O SER t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 215 through 227 removed outlier: 5.202A pdb=" N LYS t 219 " --> pdb=" O GLY t 215 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE t 220 " --> pdb=" O MET t 216 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU t 221 " --> pdb=" O GLY t 217 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG t 226 " --> pdb=" O LYS t 222 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR t 227 " --> pdb=" O HIS t 223 " (cutoff:3.500A) Processing helix chain 't' and resid 249 through 265 Processing helix chain 't' and resid 266 through 271 removed outlier: 4.220A pdb=" N THR t 270 " --> pdb=" O GLU t 266 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS t 271 " --> pdb=" O GLU t 267 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 266 through 271' Processing helix chain 't' and resid 284 through 299 Proline residue: t 299 - end of helix Processing helix chain 't' and resid 300 through 307 removed outlier: 4.926A pdb=" N HIS t 304 " --> pdb=" O LYS t 300 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU t 305 " --> pdb=" O ASP t 301 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE t 306 " --> pdb=" O PHE t 302 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU t 307 " --> pdb=" O LEU t 303 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 300 through 307' Processing helix chain 't' and resid 331 through 350 Processing helix chain 't' and resid 209 through 214 removed outlier: 4.568A pdb=" N LYS t 214 " --> pdb=" O GLY t 209 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 214' Processing sheet with id= 1, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 2, first strand: chain 'T' and resid 65 through 72 removed outlier: 4.888A pdb=" N ALA T 65 " --> pdb=" O GLU T 174 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS T 171 " --> pdb=" O ALA T 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'T' and resid 138 through 144 removed outlier: 3.893A pdb=" N GLU T 138 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR T 165 " --> pdb=" O GLY T 144 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'T' and resid 146 through 153 removed outlier: 3.601A pdb=" N LEU T 147 " --> pdb=" O LYS T 163 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG T 157 " --> pdb=" O HIS T 153 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'u' and resid 108 through 114 removed outlier: 4.976A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER u 128 " --> pdb=" O ASP u 108 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1' and resid 16 through 22 removed outlier: 5.809A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '1' and resid 41 through 46 removed outlier: 6.204A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.410A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.526A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.639A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.255A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'W' and resid 75 through 78 removed outlier: 6.748A pdb=" N VAL W 133 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'W' and resid 80 through 84 removed outlier: 7.662A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'x' and resid 130 through 133 removed outlier: 5.201A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'x' and resid 230 through 236 removed outlier: 4.040A pdb=" N TRP x 236 " --> pdb=" O ASP x 204 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASP x 250 " --> pdb=" O GLY x 302 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY x 303 " --> pdb=" O ARG x 382 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS x 379 " --> pdb=" O GLU x 339 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN x 335 " --> pdb=" O LEU x 383 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'x' and resid 361 through 365 Processing sheet with id= 18, first strand: chain '5' and resid 126 through 130 removed outlier: 5.606A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '5' and resid 208 through 214 removed outlier: 4.741A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '5' and resid 350 through 353 removed outlier: 8.219A pdb=" N ARG 5 350 " --> pdb=" O LEU 5 382 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.327A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.377A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '6' and resid 184 through 187 removed outlier: 4.317A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '6' and resid 189 through 192 removed outlier: 6.826A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '6' and resid 215 through 218 removed outlier: 3.644A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '6' and resid 272 through 276 removed outlier: 6.739A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP 6 276 " --> pdb=" O THR 6 310 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 28, first strand: chain 'z' and resid 107 through 111 removed outlier: 5.096A pdb=" N ASN z 107 " --> pdb=" O HIS z 78 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL z 151 " --> pdb=" O VAL z 55 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP z 57 " --> pdb=" O VAL z 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR z 203 " --> pdb=" O VAL z 148 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY z 150 " --> pdb=" O THR z 203 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY z 205 " --> pdb=" O GLY z 150 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'z' and resid 280 through 283 Processing sheet with id= 30, first strand: chain '7' and resid 77 through 82 removed outlier: 4.210A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '7' and resid 163 through 167 removed outlier: 6.616A pdb=" N MET 7 163 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '7' and resid 216 through 221 Processing sheet with id= 33, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.190A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'a' and resid 45 through 52 removed outlier: 5.857A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '9' and resid 42 through 45 removed outlier: 3.663A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.551A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 38, first strand: chain 'c' and resid 269 through 274 removed outlier: 3.842A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'd' and resid 212 through 219 removed outlier: 6.853A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.768A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY D 179 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU D 164 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 190 through 194 removed outlier: 4.385A pdb=" N THR D 191 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 139 through 144 Processing sheet with id= 43, first strand: chain 'e' and resid 174 through 178 removed outlier: 6.220A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.694A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU e 197 " --> pdb=" O SER e 244 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR e 240 " --> pdb=" O GLU e 201 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'e' and resid 44 through 55 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 47, first strand: chain 'E' and resid 105 through 111 removed outlier: 4.006A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'E' and resid 127 through 130 removed outlier: 6.882A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'f' and resid 126 through 135 Processing sheet with id= 50, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 51, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 52, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.411A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'H' and resid 55 through 58 removed outlier: 6.960A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 55, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.614A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.537A pdb=" N ALA J 18 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE J 67 " --> pdb=" O ALA J 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE J 71 " --> pdb=" O PHE J 79 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER J 77 " --> pdb=" O GLN J 73 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.317A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 49 through 55 removed outlier: 3.894A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 60, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 61, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 62, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 63, first strand: chain 'm' and resid 62 through 66 removed outlier: 4.783A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 65, first strand: chain 'N' and resid 118 through 123 removed outlier: 6.834A pdb=" N VAL N 160 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL N 161 " --> pdb=" O LEU N 89 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA N 186 " --> pdb=" O GLY N 92 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.161A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 79 through 83 Processing sheet with id= 68, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.379A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Q' and resid 129 through 135 removed outlier: 3.905A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 139 through 142 removed outlier: 4.031A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'r' and resid 35 through 42 removed outlier: 5.320A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 's' and resid 90 through 93 removed outlier: 4.460A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS s 204 " --> pdb=" O PRO s 237 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 's' and resid 112 through 116 removed outlier: 6.786A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 's' and resid 198 through 202 removed outlier: 6.711A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'S' and resid 105 through 109 removed outlier: 7.188A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'S' and resid 111 through 117 removed outlier: 3.897A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.664A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.042A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 't' and resid 106 through 109 removed outlier: 6.446A pdb=" N PHE t 131 " --> pdb=" O GLY t 31 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY t 29 " --> pdb=" O PRO t 133 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS t 135 " --> pdb=" O SER t 27 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N SER t 27 " --> pdb=" O LYS t 135 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN t 137 " --> pdb=" O GLY t 25 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL t 45 " --> pdb=" O VAL t 118 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP t 114 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 't' and resid 186 through 192 removed outlier: 4.008A pdb=" N LYS t 196 " --> pdb=" O TYR t 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N HIS t 320 " --> pdb=" O ALA t 273 " (cutoff:3.500A) 3127 hydrogen bonds defined for protein. 9291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 879 hydrogen bonds 1518 hydrogen bond angles 0 basepair planarities 360 basepair parallelities 744 stacking parallelities Total time for adding SS restraints: 64.27 Time building geometry restraints manager: 37.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14505 1.31 - 1.44: 39072 1.44 - 1.57: 57017 1.57 - 1.70: 2984 1.70 - 1.82: 507 Bond restraints: 114085 Sorted by residual: bond pdb=" C1' GNP t1000 " pdb=" C2' GNP t1000 " ideal model delta sigma weight residual 1.273 1.532 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C1' GNP z 401 " pdb=" C2' GNP z 401 " ideal model delta sigma weight residual 1.273 1.529 -0.256 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3' GNP z 401 " pdb=" C4' GNP z 401 " ideal model delta sigma weight residual 1.285 1.526 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C3' GNP t1000 " pdb=" C4' GNP t1000 " ideal model delta sigma weight residual 1.285 1.525 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1' SAM x 401 " pdb=" C2' SAM x 401 " ideal model delta sigma weight residual 1.307 1.520 -0.213 2.00e-02 2.50e+03 1.13e+02 ... (remaining 114080 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 11483 106.40 - 113.32: 63084 113.32 - 120.23: 40926 120.23 - 127.14: 41908 127.14 - 134.05: 4188 Bond angle restraints: 161589 Sorted by residual: angle pdb=" N PRO t 173 " pdb=" CA PRO t 173 " pdb=" CB PRO t 173 " ideal model delta sigma weight residual 103.23 110.49 -7.26 6.70e-01 2.23e+00 1.18e+02 angle pdb=" N PRO k 62 " pdb=" CA PRO k 62 " pdb=" CB PRO k 62 " ideal model delta sigma weight residual 103.23 110.23 -7.00 6.70e-01 2.23e+00 1.09e+02 angle pdb=" N PRO J 63 " pdb=" CA PRO J 63 " pdb=" CB PRO J 63 " ideal model delta sigma weight residual 103.25 113.45 -10.20 1.05e+00 9.07e-01 9.44e+01 angle pdb=" N PRO t 157 " pdb=" CA PRO t 157 " pdb=" CB PRO t 157 " ideal model delta sigma weight residual 103.31 110.97 -7.66 8.90e-01 1.26e+00 7.41e+01 angle pdb=" N PRO N 153 " pdb=" CA PRO N 153 " pdb=" CB PRO N 153 " ideal model delta sigma weight residual 103.36 110.41 -7.05 8.30e-01 1.45e+00 7.22e+01 ... (remaining 161584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 65959 35.87 - 71.73: 2492 71.73 - 107.60: 470 107.60 - 143.46: 12 143.46 - 179.33: 25 Dihedral angle restraints: 68958 sinusoidal: 40635 harmonic: 28323 Sorted by residual: dihedral pdb=" O4' U A3102 " pdb=" C1' U A3102 " pdb=" N1 U A3102 " pdb=" C2 U A3102 " ideal model delta sinusoidal sigma weight residual 200.00 26.15 173.85 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A3201 " pdb=" C1' C A3201 " pdb=" N1 C A3201 " pdb=" C2 C A3201 " ideal model delta sinusoidal sigma weight residual 200.00 29.58 170.42 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual -160.00 9.48 -169.48 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 68955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 17219 0.059 - 0.118: 1647 0.118 - 0.178: 95 0.178 - 0.237: 34 0.237 - 0.296: 11 Chirality restraints: 19006 Sorted by residual: chirality pdb=" CA PRO J 63 " pdb=" N PRO J 63 " pdb=" C PRO J 63 " pdb=" CB PRO J 63 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA PRO N 184 " pdb=" N PRO N 184 " pdb=" C PRO N 184 " pdb=" CB PRO N 184 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PRO J 125 " pdb=" N PRO J 125 " pdb=" C PRO J 125 " pdb=" CB PRO J 125 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 19003 not shown) Planarity restraints: 15355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP t1000 " 0.458 2.00e-02 2.50e+03 5.83e-01 7.65e+03 pdb=" C2' GNP t1000 " -0.615 2.00e-02 2.50e+03 pdb=" C3' GNP t1000 " -0.257 2.00e-02 2.50e+03 pdb=" C4' GNP t1000 " 0.204 2.00e-02 2.50e+03 pdb=" C5' GNP t1000 " -0.885 2.00e-02 2.50e+03 pdb=" N9 GNP t1000 " -0.017 2.00e-02 2.50e+03 pdb=" O2' GNP t1000 " -0.512 2.00e-02 2.50e+03 pdb=" O3' GNP t1000 " 0.795 2.00e-02 2.50e+03 pdb=" O4' GNP t1000 " 0.828 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP z 401 " -0.440 2.00e-02 2.50e+03 5.58e-01 7.02e+03 pdb=" C2' GNP z 401 " 0.617 2.00e-02 2.50e+03 pdb=" C3' GNP z 401 " 0.244 2.00e-02 2.50e+03 pdb=" C4' GNP z 401 " -0.222 2.00e-02 2.50e+03 pdb=" C5' GNP z 401 " 0.828 2.00e-02 2.50e+03 pdb=" N9 GNP z 401 " 0.021 2.00e-02 2.50e+03 pdb=" O2' GNP z 401 " 0.495 2.00e-02 2.50e+03 pdb=" O3' GNP z 401 " -0.806 2.00e-02 2.50e+03 pdb=" O4' GNP z 401 " -0.737 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SAM x 401 " -0.361 2.00e-02 2.50e+03 3.76e-01 3.18e+03 pdb=" C2' SAM x 401 " 0.414 2.00e-02 2.50e+03 pdb=" C3' SAM x 401 " 0.457 2.00e-02 2.50e+03 pdb=" C4' SAM x 401 " -0.363 2.00e-02 2.50e+03 pdb=" C5' SAM x 401 " 0.323 2.00e-02 2.50e+03 pdb=" N9 SAM x 401 " 0.421 2.00e-02 2.50e+03 pdb=" O2' SAM x 401 " -0.251 2.00e-02 2.50e+03 pdb=" O3' SAM x 401 " -0.120 2.00e-02 2.50e+03 pdb=" O4' SAM x 401 " -0.521 2.00e-02 2.50e+03 ... (remaining 15352 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 1028 2.58 - 3.22: 97867 3.22 - 3.86: 230174 3.86 - 4.50: 310898 4.50 - 5.14: 456652 Nonbonded interactions: 1096619 Sorted by model distance: nonbonded pdb=" O5' G A2019 " pdb="MG MG A6158 " model vdw 1.939 2.170 nonbonded pdb=" OP2 G A2496 " pdb="MG MG A6115 " model vdw 1.983 2.170 nonbonded pdb=" OP2 G A1776 " pdb="MG MG A6136 " model vdw 1.994 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A6192 " model vdw 1.999 2.170 nonbonded pdb=" OP2 U A2475 " pdb="MG MG A6196 " model vdw 2.004 2.170 ... (remaining 1096614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 24.460 Check model and map are aligned: 1.130 Set scattering table: 0.710 Process input model: 301.780 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.003 0.259 114085 Z= 0.216 Angle : 0.504 12.076 161589 Z= 0.279 Chirality : 0.036 0.296 19006 Planarity : 0.008 0.583 15355 Dihedral : 16.776 179.330 50623 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 1.05 % Allowed : 3.82 % Favored : 95.13 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 9604 helix: 2.07 (0.09), residues: 3486 sheet: 0.31 (0.14), residues: 1373 loop : 0.49 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 81 HIS 0.004 0.001 HIS z 34 PHE 0.013 0.001 PHE d 145 TYR 0.018 0.001 TYR 5 176 ARG 0.005 0.000 ARG t 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2060 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1977 time to evaluate : 7.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 155 ARG cc_start: 0.8815 (mtt-85) cc_final: 0.8614 (mtt-85) REVERT: u 157 VAL cc_start: 0.8165 (t) cc_final: 0.7949 (m) REVERT: u 200 ASP cc_start: 0.7842 (t70) cc_final: 0.7539 (t0) REVERT: 1 58 GLU cc_start: 0.6311 (tt0) cc_final: 0.5949 (tt0) REVERT: 1 61 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7816 (ttmt) REVERT: U 138 GLN cc_start: 0.6892 (mt0) cc_final: 0.6565 (mp10) REVERT: v 28 ARG cc_start: 0.6679 (mmt180) cc_final: 0.5741 (mmt90) REVERT: v 60 VAL cc_start: 0.6742 (t) cc_final: 0.6477 (t) REVERT: V 136 ARG cc_start: 0.6888 (mpp80) cc_final: 0.6676 (mtt180) REVERT: V 154 ILE cc_start: 0.7618 (pt) cc_final: 0.6360 (tp) REVERT: w 86 VAL cc_start: 0.6038 (p) cc_final: 0.4818 (p) REVERT: w 105 MET cc_start: 0.4967 (mpp) cc_final: 0.4746 (mpp) REVERT: w 119 ILE cc_start: 0.7116 (mm) cc_final: 0.6574 (mt) REVERT: w 122 MET cc_start: 0.7607 (ppp) cc_final: 0.7002 (tpt) REVERT: W 88 CYS cc_start: 0.7120 (t) cc_final: 0.6860 (t) REVERT: x 179 ASP cc_start: 0.7348 (t70) cc_final: 0.6938 (t70) REVERT: x 235 SER cc_start: 0.7905 (p) cc_final: 0.7640 (m) REVERT: 5 183 ASN cc_start: 0.7992 (m110) cc_final: 0.7664 (m110) REVERT: X 53 ASN cc_start: 0.8121 (t0) cc_final: 0.7703 (t0) REVERT: y 100 LEU cc_start: 0.7696 (mt) cc_final: 0.7200 (mt) REVERT: y 126 ASP cc_start: 0.8113 (m-30) cc_final: 0.7402 (m-30) REVERT: y 177 LYS cc_start: 0.7966 (tttm) cc_final: 0.7352 (ttmm) REVERT: y 234 PHE cc_start: 0.8301 (t80) cc_final: 0.7800 (t80) REVERT: 6 148 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8251 (tttt) REVERT: 6 151 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8586 (mp) REVERT: 6 273 PHE cc_start: 0.7689 (m-10) cc_final: 0.7348 (m-10) REVERT: Y 76 GLN cc_start: 0.7639 (mt0) cc_final: 0.7180 (tt0) REVERT: Y 87 CYS cc_start: 0.5716 (m) cc_final: 0.5181 (m) REVERT: z 31 PHE cc_start: 0.7578 (t80) cc_final: 0.7275 (t80) REVERT: z 153 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7436 (t0) REVERT: z 298 TYR cc_start: 0.7835 (m-80) cc_final: 0.7578 (m-80) REVERT: Z 52 ASP cc_start: 0.8269 (m-30) cc_final: 0.8046 (m-30) REVERT: Z 84 ASP cc_start: 0.7829 (m-30) cc_final: 0.7626 (m-30) REVERT: Z 87 LYS cc_start: 0.8283 (tptp) cc_final: 0.7737 (tptp) REVERT: c 52 ARG cc_start: 0.7627 (tmm-80) cc_final: 0.7258 (tmm-80) REVERT: d 74 ARG cc_start: 0.7649 (ttt180) cc_final: 0.7443 (ttt90) REVERT: D 128 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7160 (tt0) REVERT: e 70 MET cc_start: 0.5509 (mtt) cc_final: 0.5122 (mtt) REVERT: e 88 GLU cc_start: 0.6325 (mm-30) cc_final: 0.5592 (mm-30) REVERT: e 141 ASP cc_start: 0.3275 (m-30) cc_final: 0.2888 (t70) REVERT: e 145 ASP cc_start: 0.6820 (m-30) cc_final: 0.6508 (m-30) REVERT: e 257 LYS cc_start: 0.1698 (tttp) cc_final: 0.0587 (tttp) REVERT: e 258 ASP cc_start: 0.5682 (m-30) cc_final: 0.5328 (t0) REVERT: E 336 ASN cc_start: 0.6853 (m-40) cc_final: 0.6592 (m110) REVERT: f 101 THR cc_start: 0.6785 (p) cc_final: 0.6503 (m) REVERT: f 165 THR cc_start: 0.7263 (p) cc_final: 0.6902 (t) REVERT: f 176 SER cc_start: 0.6939 (t) cc_final: 0.6506 (m) REVERT: f 202 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.7959 (Cg_exo) REVERT: F 184 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: F 218 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7636 (mt) REVERT: F 295 ARG cc_start: 0.6375 (ttm-80) cc_final: 0.6073 (mtp180) REVERT: I 60 ILE cc_start: 0.6817 (mm) cc_final: 0.6571 (tp) REVERT: i 53 MET cc_start: 0.8609 (mmp) cc_final: 0.8341 (mmp) REVERT: M 11 ARG cc_start: 0.6995 (ptp90) cc_final: 0.6617 (ttp-110) REVERT: m 62 SER cc_start: 0.6166 (p) cc_final: 0.5950 (p) REVERT: N 231 SER cc_start: 0.8514 (t) cc_final: 0.8300 (t) REVERT: o 27 VAL cc_start: 0.9197 (m) cc_final: 0.8938 (t) REVERT: O 154 GLN cc_start: 0.8573 (mt0) cc_final: 0.8269 (mt0) REVERT: P 117 TYR cc_start: 0.6784 (t80) cc_final: 0.6314 (t80) REVERT: P 166 THR cc_start: 0.8543 (m) cc_final: 0.8304 (p) REVERT: Q 259 LYS cc_start: 0.8418 (mttm) cc_final: 0.8081 (mtpt) REVERT: Q 269 MET cc_start: 0.8492 (ptp) cc_final: 0.8247 (ptm) REVERT: r 111 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6638 (tp30) REVERT: r 117 GLU cc_start: 0.7987 (tp30) cc_final: 0.7490 (tp30) REVERT: r 121 MET cc_start: 0.8973 (mtp) cc_final: 0.8599 (mtp) REVERT: t 48 VAL cc_start: 0.6978 (t) cc_final: 0.6357 (t) REVERT: t 111 LYS cc_start: 0.6425 (tptp) cc_final: 0.6196 (ttpp) REVERT: t 112 GLU cc_start: 0.7196 (tt0) cc_final: 0.6657 (tt0) REVERT: t 120 GLN cc_start: 0.8548 (mt0) cc_final: 0.8156 (mp10) REVERT: t 139 ARG cc_start: 0.6786 (mpt90) cc_final: 0.5580 (mmm-85) REVERT: t 141 ILE cc_start: 0.8105 (pt) cc_final: 0.7638 (tp) outliers start: 83 outliers final: 28 residues processed: 2034 average time/residue: 0.9849 time to fit residues: 3389.2874 Evaluate side-chains 1377 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1345 time to evaluate : 7.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain 6 residue 151 LEU Chi-restraints excluded: chain z residue 73 LEU Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 153 ASN Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain t residue 94 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 930 optimal weight: 7.9990 chunk 835 optimal weight: 0.2980 chunk 463 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 563 optimal weight: 0.0670 chunk 446 optimal weight: 10.0000 chunk 863 optimal weight: 10.0000 chunk 334 optimal weight: 0.7980 chunk 525 optimal weight: 20.0000 chunk 642 optimal weight: 30.0000 chunk 1000 optimal weight: 4.9990 overall best weight: 2.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 113 GLN V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 GLN x 230 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN X 76 GLN 6 63 GLN 6 239 ASN ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 ASN 7 298 GLN a 137 ASN 9 90 GLN b 24 GLN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN d 59 HIS d 153 ASN d 154 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN F 98 GLN F 105 ASN H 93 ASN K 9 GLN L 72 GLN o 46 HIS o 91 GLN p 143 GLN p 176 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 120 HIS Q 139 GLN r 130 ASN s 152 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 197 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 114085 Z= 0.233 Angle : 0.568 21.270 161589 Z= 0.274 Chirality : 0.037 0.234 19006 Planarity : 0.004 0.049 15355 Dihedral : 18.638 178.752 31809 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 2.33 % Allowed : 9.23 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.09), residues: 9604 helix: 1.97 (0.09), residues: 3475 sheet: 0.21 (0.14), residues: 1366 loop : 0.41 (0.09), residues: 4763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 275 HIS 0.009 0.001 HIS p 176 PHE 0.030 0.002 PHE v 32 TYR 0.022 0.001 TYR U 56 ARG 0.008 0.000 ARG u 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1378 time to evaluate : 7.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 144 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8225 (ptpp) REVERT: u 202 GLN cc_start: 0.5781 (mt0) cc_final: 0.5531 (mt0) REVERT: U 138 GLN cc_start: 0.7023 (mt0) cc_final: 0.6692 (mp10) REVERT: v 28 ARG cc_start: 0.6842 (mmt180) cc_final: 0.5930 (mmt90) REVERT: V 136 ARG cc_start: 0.7071 (mpp80) cc_final: 0.6805 (mtt180) REVERT: w 86 VAL cc_start: 0.6385 (p) cc_final: 0.5255 (p) REVERT: w 122 MET cc_start: 0.7684 (ppp) cc_final: 0.7108 (tpt) REVERT: w 123 GLU cc_start: 0.6452 (tt0) cc_final: 0.5962 (tt0) REVERT: x 275 ARG cc_start: 0.6602 (ttt180) cc_final: 0.6352 (ttt90) REVERT: 5 183 ASN cc_start: 0.8179 (m110) cc_final: 0.7808 (m-40) REVERT: y 134 LEU cc_start: 0.8728 (mt) cc_final: 0.8468 (tt) REVERT: y 139 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7844 (pp20) REVERT: y 177 LYS cc_start: 0.7986 (tttm) cc_final: 0.7388 (ttmt) REVERT: Y 76 GLN cc_start: 0.7684 (mt0) cc_final: 0.7305 (tt0) REVERT: z 109 ILE cc_start: 0.8772 (mm) cc_final: 0.8520 (mt) REVERT: z 298 TYR cc_start: 0.7850 (m-80) cc_final: 0.7594 (m-80) REVERT: z 318 MET cc_start: 0.6623 (tpp) cc_final: 0.6388 (tpp) REVERT: Z 84 ASP cc_start: 0.7879 (m-30) cc_final: 0.7630 (m-30) REVERT: 8 144 GLN cc_start: 0.8168 (tp40) cc_final: 0.7886 (tm-30) REVERT: 8 163 LYS cc_start: 0.7512 (tptt) cc_final: 0.7263 (ptmm) REVERT: c 52 ARG cc_start: 0.7574 (tmm-80) cc_final: 0.7264 (tmm-80) REVERT: D 113 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7398 (ttm170) REVERT: D 128 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7341 (tt0) REVERT: e 70 MET cc_start: 0.5674 (mtt) cc_final: 0.5319 (mtt) REVERT: e 141 ASP cc_start: 0.3145 (m-30) cc_final: 0.2736 (t70) REVERT: E 336 ASN cc_start: 0.6998 (m-40) cc_final: 0.6738 (m110) REVERT: f 176 SER cc_start: 0.6886 (t) cc_final: 0.6487 (m) REVERT: f 206 GLU cc_start: 0.7430 (tt0) cc_final: 0.7223 (tp30) REVERT: F 70 ARG cc_start: 0.7050 (ttm110) cc_final: 0.6783 (mtp85) REVERT: F 184 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: H 95 GLU cc_start: 0.7930 (tt0) cc_final: 0.7729 (tt0) REVERT: H 138 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7909 (tppp) REVERT: H 142 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7335 (mt-10) REVERT: i 53 MET cc_start: 0.8510 (mmp) cc_final: 0.8277 (mmp) REVERT: L 86 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8297 (tt) REVERT: o 27 VAL cc_start: 0.9213 (m) cc_final: 0.8936 (t) REVERT: P 117 TYR cc_start: 0.6844 (t80) cc_final: 0.6037 (t80) REVERT: P 134 GLN cc_start: 0.8782 (tp40) cc_final: 0.8457 (tp40) REVERT: P 166 THR cc_start: 0.8552 (m) cc_final: 0.8351 (p) REVERT: q 44 ASP cc_start: 0.8124 (t0) cc_final: 0.7787 (t0) REVERT: r 117 GLU cc_start: 0.8105 (tp30) cc_final: 0.7497 (tp30) REVERT: r 121 MET cc_start: 0.9073 (mtp) cc_final: 0.8608 (mtp) REVERT: R 100 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7994 (ttpt) REVERT: s 341 MET cc_start: 0.8288 (mmm) cc_final: 0.8084 (mmm) REVERT: t 111 LYS cc_start: 0.6653 (tptp) cc_final: 0.6360 (ttpp) REVERT: t 112 GLU cc_start: 0.7355 (tt0) cc_final: 0.6794 (tt0) REVERT: t 117 LEU cc_start: 0.8231 (tp) cc_final: 0.8003 (tt) REVERT: t 120 GLN cc_start: 0.8525 (mt0) cc_final: 0.8189 (mp10) REVERT: t 139 ARG cc_start: 0.6775 (mpt90) cc_final: 0.5693 (mmm-85) REVERT: t 141 ILE cc_start: 0.7919 (pt) cc_final: 0.7383 (tp) outliers start: 184 outliers final: 112 residues processed: 1485 average time/residue: 0.9641 time to fit residues: 2458.3409 Evaluate side-chains 1381 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1265 time to evaluate : 7.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 109 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 168 GLU Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 259 THR Chi-restraints excluded: chain z residue 73 LEU Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 198 ASN Chi-restraints excluded: chain 8 residue 111 THR Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 122 SER Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 556 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 832 optimal weight: 40.0000 chunk 681 optimal weight: 0.9980 chunk 276 optimal weight: 10.0000 chunk 1002 optimal weight: 9.9990 chunk 1083 optimal weight: 40.0000 chunk 892 optimal weight: 0.0030 chunk 994 optimal weight: 0.8980 chunk 341 optimal weight: 6.9990 chunk 804 optimal weight: 6.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN 5 384 GLN z 295 GLN ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN Z 61 GLN 8 127 GLN 8 143 GLN 8 177 HIS a 71 HIS ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 107 GLN d 154 ASN e 207 ASN F 105 ASN o 46 HIS p 176 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 114085 Z= 0.252 Angle : 0.571 20.783 161589 Z= 0.278 Chirality : 0.038 0.231 19006 Planarity : 0.004 0.051 15355 Dihedral : 18.629 179.131 31802 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.75 % Allowed : 10.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 9604 helix: 1.81 (0.09), residues: 3495 sheet: 0.15 (0.14), residues: 1365 loop : 0.31 (0.09), residues: 4744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP 8 121 HIS 0.008 0.001 HIS p 176 PHE 0.020 0.001 PHE d 145 TYR 0.028 0.001 TYR v 31 ARG 0.011 0.000 ARG z 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1317 time to evaluate : 7.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 169 ASP cc_start: 0.8277 (t70) cc_final: 0.7878 (t0) REVERT: u 107 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7235 (mmt90) REVERT: u 108 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7365 (t0) REVERT: u 144 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8158 (ptpp) REVERT: u 152 LYS cc_start: 0.6816 (pttm) cc_final: 0.6378 (mttp) REVERT: U 138 GLN cc_start: 0.7054 (mt0) cc_final: 0.6671 (mp10) REVERT: v 28 ARG cc_start: 0.6761 (mmt180) cc_final: 0.5825 (mmt90) REVERT: V 136 ARG cc_start: 0.7131 (mpp80) cc_final: 0.6922 (mtm180) REVERT: w 86 VAL cc_start: 0.6645 (p) cc_final: 0.5012 (p) REVERT: w 122 MET cc_start: 0.7678 (ppp) cc_final: 0.7238 (tpp) REVERT: W 127 TYR cc_start: 0.8014 (m-80) cc_final: 0.7790 (m-80) REVERT: x 244 LEU cc_start: 0.6412 (mt) cc_final: 0.5967 (mt) REVERT: x 275 ARG cc_start: 0.6716 (ttt180) cc_final: 0.6480 (ttt90) REVERT: 5 183 ASN cc_start: 0.8217 (m110) cc_final: 0.7810 (m110) REVERT: 5 313 MET cc_start: 0.8447 (mtp) cc_final: 0.8240 (mtt) REVERT: y 139 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: y 177 LYS cc_start: 0.8045 (tttm) cc_final: 0.7364 (ttmm) REVERT: Y 76 GLN cc_start: 0.7726 (mt0) cc_final: 0.7365 (tt0) REVERT: z 109 ILE cc_start: 0.8760 (mm) cc_final: 0.8543 (mt) REVERT: z 202 ASP cc_start: 0.7998 (t0) cc_final: 0.7796 (t0) REVERT: z 298 TYR cc_start: 0.7795 (m-80) cc_final: 0.7457 (m-80) REVERT: Z 84 ASP cc_start: 0.7890 (m-30) cc_final: 0.7556 (m-30) REVERT: 8 144 GLN cc_start: 0.8141 (tp40) cc_final: 0.7831 (tm-30) REVERT: b 50 GLU cc_start: 0.7559 (tp30) cc_final: 0.7202 (tp30) REVERT: c 52 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.7280 (tmm-80) REVERT: D 113 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7515 (ttm170) REVERT: D 128 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7402 (tt0) REVERT: e 141 ASP cc_start: 0.2967 (m-30) cc_final: 0.2587 (t70) REVERT: E 225 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6443 (tttt) REVERT: E 336 ASN cc_start: 0.7158 (m-40) cc_final: 0.6878 (m110) REVERT: f 116 SER cc_start: 0.8600 (m) cc_final: 0.8261 (t) REVERT: f 176 SER cc_start: 0.6837 (t) cc_final: 0.6521 (m) REVERT: F 70 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6809 (mtp85) REVERT: F 184 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: H 95 GLU cc_start: 0.7998 (tt0) cc_final: 0.7745 (tt0) REVERT: H 138 LYS cc_start: 0.7709 (mmmt) cc_final: 0.6938 (tptp) REVERT: h 119 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7553 (tm-30) REVERT: I 60 ILE cc_start: 0.6905 (mm) cc_final: 0.6625 (mm) REVERT: i 84 LYS cc_start: 0.8447 (tttp) cc_final: 0.8231 (tttt) REVERT: L 86 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8240 (tt) REVERT: o 27 VAL cc_start: 0.9223 (m) cc_final: 0.8899 (t) REVERT: P 134 GLN cc_start: 0.8747 (tp40) cc_final: 0.8466 (tp40) REVERT: q 44 ASP cc_start: 0.8279 (t0) cc_final: 0.7906 (t0) REVERT: r 117 GLU cc_start: 0.8125 (tp30) cc_final: 0.7541 (tp30) REVERT: R 100 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8174 (ttpt) REVERT: s 341 MET cc_start: 0.8272 (mmm) cc_final: 0.8040 (mmm) REVERT: t 111 LYS cc_start: 0.6656 (tptp) cc_final: 0.6338 (ttpp) REVERT: t 112 GLU cc_start: 0.7439 (tt0) cc_final: 0.6798 (tt0) REVERT: t 139 ARG cc_start: 0.6731 (mpt90) cc_final: 0.5713 (mmm-85) REVERT: t 141 ILE cc_start: 0.7966 (pt) cc_final: 0.7370 (tp) outliers start: 217 outliers final: 151 residues processed: 1447 average time/residue: 0.9754 time to fit residues: 2442.7700 Evaluate side-chains 1390 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1234 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 174 SER Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 118 ILE Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 140 SER Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 168 GLU Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 259 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 326 SER Chi-restraints excluded: chain z residue 73 LEU Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 293 ILE Chi-restraints excluded: chain z residue 295 GLN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 198 ASN Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 122 SER Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 310 ASN Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 185 ARG Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 404 THR Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain s residue 407 ASP Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 38 GLU Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 990 optimal weight: 10.0000 chunk 753 optimal weight: 0.5980 chunk 520 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 478 optimal weight: 10.0000 chunk 673 optimal weight: 20.0000 chunk 1006 optimal weight: 3.9990 chunk 1065 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 953 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 GLN x 55 GLN x 218 HIS x 371 ASN 5 251 HIS 5 384 GLN X 4 HIS X 15 GLN X 76 GLN y 192 GLN ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 69 HIS ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 198 ASN 7 298 GLN Z 61 GLN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN d 154 ASN F 105 ASN H 93 ASN H 100 GLN L 59 HIS L 72 GLN o 46 HIS p 176 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 190 GLN ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 152 GLN s 246 GLN s 387 ASN S 91 GLN t 120 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 114085 Z= 0.409 Angle : 0.685 21.129 161589 Z= 0.339 Chirality : 0.043 0.243 19006 Planarity : 0.005 0.065 15355 Dihedral : 18.792 178.529 31801 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 3.89 % Allowed : 11.55 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.08), residues: 9604 helix: 1.32 (0.09), residues: 3486 sheet: -0.01 (0.14), residues: 1335 loop : 0.01 (0.09), residues: 4783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP 8 121 HIS 0.010 0.002 HIS y 265 PHE 0.028 0.002 PHE d 145 TYR 0.031 0.002 TYR v 31 ARG 0.010 0.001 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1265 time to evaluate : 7.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 107 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7173 (mpt-90) REVERT: u 118 MET cc_start: 0.7700 (mmm) cc_final: 0.7081 (mmt) REVERT: u 119 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6504 (mtp180) REVERT: u 152 LYS cc_start: 0.7099 (pttm) cc_final: 0.6630 (mttp) REVERT: u 189 GLU cc_start: 0.7980 (pm20) cc_final: 0.7763 (pm20) REVERT: v 28 ARG cc_start: 0.6566 (mmt180) cc_final: 0.5600 (mmt90) REVERT: V 23 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8233 (mmm) REVERT: V 56 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8207 (mt) REVERT: V 118 ARG cc_start: 0.7637 (mpt-90) cc_final: 0.7282 (mpt-90) REVERT: V 136 ARG cc_start: 0.7355 (mpp80) cc_final: 0.7023 (mtm180) REVERT: W 127 TYR cc_start: 0.7920 (m-80) cc_final: 0.7618 (m-80) REVERT: x 42 ARG cc_start: 0.7645 (ttt180) cc_final: 0.7342 (ttt180) REVERT: 5 183 ASN cc_start: 0.8330 (m110) cc_final: 0.7969 (m110) REVERT: X 221 LYS cc_start: 0.8506 (mppt) cc_final: 0.8007 (mptt) REVERT: y 139 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: y 177 LYS cc_start: 0.8086 (tttm) cc_final: 0.7451 (ttmt) REVERT: y 267 TYR cc_start: 0.8591 (t80) cc_final: 0.8389 (t80) REVERT: y 295 ARG cc_start: 0.6945 (tpt170) cc_final: 0.6532 (tpt170) REVERT: Y 76 GLN cc_start: 0.7909 (mt0) cc_final: 0.7669 (tt0) REVERT: Y 204 TYR cc_start: 0.8658 (p90) cc_final: 0.8387 (p90) REVERT: z 109 ILE cc_start: 0.8740 (mm) cc_final: 0.8535 (mt) REVERT: z 202 ASP cc_start: 0.8105 (t0) cc_final: 0.7885 (t0) REVERT: 7 124 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: 7 143 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.6954 (m-90) REVERT: Z 84 ASP cc_start: 0.7883 (m-30) cc_final: 0.7602 (m-30) REVERT: 8 117 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7960 (pp) REVERT: 8 139 MET cc_start: 0.6254 (mtp) cc_final: 0.5868 (mtm) REVERT: 8 144 GLN cc_start: 0.8044 (tp40) cc_final: 0.7576 (tm-30) REVERT: b 50 GLU cc_start: 0.7669 (tp30) cc_final: 0.7339 (tp30) REVERT: c 309 GLU cc_start: 0.7075 (mp0) cc_final: 0.6870 (mp0) REVERT: D 113 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7571 (ttm170) REVERT: D 128 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7340 (tt0) REVERT: D 131 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7823 (t80) REVERT: e 136 ARG cc_start: 0.5315 (mtp180) cc_final: 0.5108 (mtp180) REVERT: e 141 ASP cc_start: 0.3491 (m-30) cc_final: 0.3021 (t70) REVERT: e 259 GLU cc_start: 0.3014 (OUTLIER) cc_final: 0.2738 (pm20) REVERT: E 135 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7712 (ttpp) REVERT: F 49 ARG cc_start: 0.8359 (tmt170) cc_final: 0.8120 (tmt170) REVERT: F 184 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: I 65 LEU cc_start: 0.7253 (mt) cc_final: 0.6956 (mt) REVERT: L 86 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8414 (tt) REVERT: M 57 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.8229 (ptp-170) REVERT: N 215 PHE cc_start: 0.8619 (t80) cc_final: 0.8381 (t80) REVERT: o 33 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: p 181 GLU cc_start: 0.7762 (pt0) cc_final: 0.7393 (pt0) REVERT: P 134 GLN cc_start: 0.8865 (tp40) cc_final: 0.8599 (tp40) REVERT: q 44 ASP cc_start: 0.8392 (t0) cc_final: 0.8094 (t0) REVERT: r 117 GLU cc_start: 0.8212 (tp30) cc_final: 0.7715 (tp30) REVERT: r 121 MET cc_start: 0.9081 (mtp) cc_final: 0.7904 (mtm) REVERT: r 149 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7430 (ptp-170) REVERT: s 341 MET cc_start: 0.8356 (mmm) cc_final: 0.8066 (mmm) REVERT: t 100 ASP cc_start: 0.5204 (t0) cc_final: 0.4975 (t0) REVERT: t 111 LYS cc_start: 0.6763 (tptp) cc_final: 0.6384 (ttpp) REVERT: t 112 GLU cc_start: 0.7483 (tt0) cc_final: 0.6689 (tt0) REVERT: t 141 ILE cc_start: 0.7999 (pt) cc_final: 0.7469 (tp) outliers start: 307 outliers final: 192 residues processed: 1470 average time/residue: 0.9588 time to fit residues: 2425.6746 Evaluate side-chains 1393 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1187 time to evaluate : 8.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 138 MET Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain U residue 27 GLN Chi-restraints excluded: chain U residue 141 ASP Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 176 ASP Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 55 GLN Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 140 SER Chi-restraints excluded: chain x residue 169 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 336 VAL Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 168 GLU Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 229 ILE Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 208 THR Chi-restraints excluded: chain y residue 259 THR Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 326 SER Chi-restraints excluded: chain z residue 73 LEU Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 243 THR Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 39 GLU Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 84 ASN Chi-restraints excluded: chain 7 residue 124 GLU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain d residue 45 ILE Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 50 ARG Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 33 GLN Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain r residue 149 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain t residue 38 GLU Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 887 optimal weight: 50.0000 chunk 604 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 793 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 908 optimal weight: 0.7980 chunk 736 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 543 optimal weight: 20.0000 chunk 956 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 18 HIS V 78 GLN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 192 GLN ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 247 HIS ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 246 GLN 7 298 GLN Z 61 GLN b 90 HIS ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 175 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** p 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 114085 Z= 0.153 Angle : 0.552 19.157 161589 Z= 0.269 Chirality : 0.036 0.232 19006 Planarity : 0.004 0.054 15355 Dihedral : 18.661 179.941 31795 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 13.26 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.09), residues: 9604 helix: 1.69 (0.09), residues: 3501 sheet: 0.15 (0.14), residues: 1315 loop : 0.19 (0.09), residues: 4788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP 8 121 HIS 0.008 0.001 HIS p 176 PHE 0.037 0.001 PHE 6 298 TYR 0.024 0.001 TYR v 31 ARG 0.006 0.000 ARG L 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1310 time to evaluate : 7.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 119 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6933 (mtp180) REVERT: u 144 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8015 (ptpp) REVERT: u 152 LYS cc_start: 0.7048 (pttm) cc_final: 0.6593 (mttp) REVERT: U 37 GLU cc_start: 0.7723 (pp20) cc_final: 0.7475 (pp20) REVERT: U 110 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (mm) REVERT: v 25 TYR cc_start: 0.6129 (m-80) cc_final: 0.5598 (m-80) REVERT: v 28 ARG cc_start: 0.6510 (mmt180) cc_final: 0.5669 (mmt90) REVERT: v 31 TYR cc_start: 0.6716 (t80) cc_final: 0.6500 (t80) REVERT: v 45 LEU cc_start: 0.6788 (pp) cc_final: 0.6538 (pp) REVERT: v 62 LEU cc_start: 0.8099 (tp) cc_final: 0.7881 (tp) REVERT: V 23 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8197 (mmm) REVERT: w 143 GLU cc_start: 0.7376 (tp30) cc_final: 0.7149 (tp30) REVERT: x 263 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: 5 183 ASN cc_start: 0.8242 (m110) cc_final: 0.7864 (m110) REVERT: X 53 ASN cc_start: 0.8421 (t0) cc_final: 0.8197 (m-40) REVERT: X 221 LYS cc_start: 0.8549 (mppt) cc_final: 0.8172 (mptt) REVERT: y 139 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: y 177 LYS cc_start: 0.8015 (tttm) cc_final: 0.7381 (ttmt) REVERT: Y 76 GLN cc_start: 0.7769 (mt0) cc_final: 0.7535 (tt0) REVERT: z 202 ASP cc_start: 0.7975 (t0) cc_final: 0.7774 (t0) REVERT: z 298 TYR cc_start: 0.7801 (m-80) cc_final: 0.7506 (m-80) REVERT: Z 84 ASP cc_start: 0.7844 (m-30) cc_final: 0.7624 (m-30) REVERT: Z 156 GLN cc_start: 0.7287 (mm110) cc_final: 0.6793 (mm-40) REVERT: 8 139 MET cc_start: 0.6235 (mtp) cc_final: 0.5854 (mtm) REVERT: 8 144 GLN cc_start: 0.8106 (tp40) cc_final: 0.7824 (tm-30) REVERT: b 50 GLU cc_start: 0.7609 (tp30) cc_final: 0.7272 (tp30) REVERT: D 128 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7205 (tt0) REVERT: e 136 ARG cc_start: 0.5187 (mtp180) cc_final: 0.4983 (mtt-85) REVERT: e 141 ASP cc_start: 0.3325 (m-30) cc_final: 0.2972 (t70) REVERT: e 259 GLU cc_start: 0.2902 (OUTLIER) cc_final: 0.2590 (pm20) REVERT: F 70 ARG cc_start: 0.7117 (ttm110) cc_final: 0.6755 (mtt90) REVERT: I 65 LEU cc_start: 0.7400 (mt) cc_final: 0.7124 (mt) REVERT: L 86 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (tt) REVERT: M 57 ARG cc_start: 0.8413 (ptp-170) cc_final: 0.8138 (ptp-170) REVERT: N 215 PHE cc_start: 0.8569 (t80) cc_final: 0.8338 (t80) REVERT: N 218 ILE cc_start: 0.8723 (mm) cc_final: 0.8498 (mt) REVERT: o 69 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: p 181 GLU cc_start: 0.7667 (pt0) cc_final: 0.7307 (pt0) REVERT: P 134 GLN cc_start: 0.8808 (tp40) cc_final: 0.8573 (tp40) REVERT: q 44 ASP cc_start: 0.8315 (t0) cc_final: 0.7960 (t0) REVERT: s 341 MET cc_start: 0.8286 (mmm) cc_final: 0.8055 (mmm) REVERT: t 111 LYS cc_start: 0.6784 (tptp) cc_final: 0.6119 (ptmm) REVERT: t 112 GLU cc_start: 0.7532 (tt0) cc_final: 0.6566 (tt0) REVERT: t 141 ILE cc_start: 0.7864 (pt) cc_final: 0.7422 (tp) outliers start: 198 outliers final: 132 residues processed: 1423 average time/residue: 0.9402 time to fit residues: 2311.0435 Evaluate side-chains 1345 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1206 time to evaluate : 7.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 174 SER Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 336 VAL Chi-restraints excluded: chain 5 residue 168 GLU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain 6 residue 63 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 247 HIS Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 150 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 185 ARG Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 165 THR Chi-restraints excluded: chain f residue 174 ILE Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 77 ASP Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 120 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 358 optimal weight: 8.9990 chunk 959 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 625 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 1066 optimal weight: 4.9990 chunk 885 optimal weight: 40.0000 chunk 493 optimal weight: 20.0000 chunk 88 optimal weight: 0.0270 chunk 352 optimal weight: 0.7980 chunk 559 optimal weight: 4.9990 overall best weight: 3.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 GLN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 384 GLN X 15 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 229 HIS ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN Z 61 GLN d 154 ASN F 103 GLN H 100 GLN K 117 HIS L 72 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** p 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 114085 Z= 0.278 Angle : 0.598 19.622 161589 Z= 0.292 Chirality : 0.039 0.232 19006 Planarity : 0.004 0.055 15355 Dihedral : 18.637 179.304 31788 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 3.15 % Allowed : 13.21 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.09), residues: 9604 helix: 1.61 (0.09), residues: 3501 sheet: 0.08 (0.14), residues: 1322 loop : 0.10 (0.09), residues: 4781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 275 HIS 0.023 0.001 HIS z 247 PHE 0.029 0.002 PHE 6 298 TYR 0.023 0.001 TYR v 31 ARG 0.009 0.000 ARG S 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1480 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1231 time to evaluate : 7.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 119 ARG cc_start: 0.7309 (mtp180) cc_final: 0.6975 (mtp180) REVERT: u 144 LYS cc_start: 0.8446 (ptmm) cc_final: 0.8024 (ptpp) REVERT: u 152 LYS cc_start: 0.7170 (pttm) cc_final: 0.6703 (mttp) REVERT: U 110 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8225 (mm) REVERT: v 25 TYR cc_start: 0.6138 (m-80) cc_final: 0.5546 (m-80) REVERT: v 28 ARG cc_start: 0.6466 (mmt180) cc_final: 0.5636 (mmt90) REVERT: v 31 TYR cc_start: 0.6885 (t80) cc_final: 0.6630 (t80) REVERT: v 45 LEU cc_start: 0.7008 (pp) cc_final: 0.6803 (pp) REVERT: V 23 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: V 136 ARG cc_start: 0.7325 (mpp80) cc_final: 0.6995 (mtm180) REVERT: w 143 GLU cc_start: 0.7439 (tp30) cc_final: 0.7181 (tp30) REVERT: x 42 ARG cc_start: 0.7598 (ttt180) cc_final: 0.7288 (ttt180) REVERT: x 164 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7877 (mp) REVERT: x 263 HIS cc_start: 0.7527 (t-90) cc_final: 0.7090 (t-90) REVERT: 5 183 ASN cc_start: 0.8258 (m110) cc_final: 0.7875 (m110) REVERT: X 33 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: X 53 ASN cc_start: 0.8547 (t0) cc_final: 0.8235 (m-40) REVERT: X 60 GLU cc_start: 0.8104 (pm20) cc_final: 0.7779 (pm20) REVERT: y 139 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: y 177 LYS cc_start: 0.8052 (tttm) cc_final: 0.7427 (ttmt) REVERT: Y 76 GLN cc_start: 0.7846 (mt0) cc_final: 0.7608 (tt0) REVERT: z 202 ASP cc_start: 0.8001 (t0) cc_final: 0.7796 (t0) REVERT: z 298 TYR cc_start: 0.7820 (m-80) cc_final: 0.7516 (m-80) REVERT: 7 143 TRP cc_start: 0.8280 (OUTLIER) cc_final: 0.7342 (m-90) REVERT: 7 163 MET cc_start: 0.6201 (ppp) cc_final: 0.6000 (ppp) REVERT: Z 84 ASP cc_start: 0.7879 (m-30) cc_final: 0.7607 (m-30) REVERT: 8 139 MET cc_start: 0.6290 (mtp) cc_final: 0.5911 (mtm) REVERT: 8 144 GLN cc_start: 0.8078 (tp40) cc_final: 0.7820 (tm-30) REVERT: b 50 GLU cc_start: 0.7724 (tp30) cc_final: 0.7433 (tp30) REVERT: D 128 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7347 (tt0) REVERT: D 131 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7866 (t80) REVERT: e 136 ARG cc_start: 0.5305 (mtp180) cc_final: 0.5026 (mtt-85) REVERT: e 141 ASP cc_start: 0.3443 (m-30) cc_final: 0.3079 (t70) REVERT: e 259 GLU cc_start: 0.2714 (OUTLIER) cc_final: 0.2455 (pm20) REVERT: F 70 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6849 (mtt90) REVERT: I 65 LEU cc_start: 0.7257 (mt) cc_final: 0.6992 (mt) REVERT: L 86 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8253 (tt) REVERT: o 33 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: o 69 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: o 72 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: p 116 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7027 (mtp85) REVERT: p 181 GLU cc_start: 0.7713 (pt0) cc_final: 0.7247 (pt0) REVERT: P 134 GLN cc_start: 0.8802 (tp40) cc_final: 0.8556 (tp40) REVERT: q 44 ASP cc_start: 0.8369 (t0) cc_final: 0.8028 (t0) REVERT: r 149 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7209 (ptp-170) REVERT: s 341 MET cc_start: 0.8297 (mmm) cc_final: 0.8057 (mmm) REVERT: t 111 LYS cc_start: 0.6788 (tptp) cc_final: 0.6397 (ttpp) REVERT: t 112 GLU cc_start: 0.7480 (tt0) cc_final: 0.6664 (tt0) REVERT: t 141 ILE cc_start: 0.7892 (pt) cc_final: 0.7443 (tp) outliers start: 249 outliers final: 177 residues processed: 1388 average time/residue: 0.9544 time to fit residues: 2288.0794 Evaluate side-chains 1378 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1187 time to evaluate : 7.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 138 MET Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain U residue 27 GLN Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 140 SER Chi-restraints excluded: chain x residue 164 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 312 LEU Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 336 VAL Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 229 ILE Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 290 LEU Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 8 residue 135 THR Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 201 GLU Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 50 ARG Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 110 LYS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 33 GLN Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 72 GLU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain r residue 149 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 387 ASN Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 1027 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 607 optimal weight: 5.9990 chunk 778 optimal weight: 0.6980 chunk 603 optimal weight: 9.9990 chunk 897 optimal weight: 0.9980 chunk 595 optimal weight: 7.9990 chunk 1062 optimal weight: 2.9990 chunk 664 optimal weight: 7.9990 chunk 647 optimal weight: 5.9990 chunk 490 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 ASN U 138 GLN V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN Z 61 GLN d 154 ASN e 219 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 114085 Z= 0.210 Angle : 0.570 19.025 161589 Z= 0.278 Chirality : 0.037 0.232 19006 Planarity : 0.004 0.055 15355 Dihedral : 18.612 179.818 31788 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 3.25 % Allowed : 13.45 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 9604 helix: 1.67 (0.09), residues: 3508 sheet: 0.07 (0.14), residues: 1329 loop : 0.13 (0.09), residues: 4767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP D 275 HIS 0.008 0.001 HIS p 176 PHE 0.029 0.001 PHE 6 298 TYR 0.022 0.001 TYR v 31 ARG 0.012 0.000 ARG S 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1251 time to evaluate : 7.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 103 GLN cc_start: 0.7980 (mp10) cc_final: 0.7754 (mp10) REVERT: u 107 ARG cc_start: 0.7250 (mpt-90) cc_final: 0.6955 (mmt90) REVERT: u 108 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7076 (t0) REVERT: u 152 LYS cc_start: 0.7116 (pttm) cc_final: 0.6702 (mttp) REVERT: 1 23 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7820 (mt-10) REVERT: U 37 GLU cc_start: 0.7778 (pp20) cc_final: 0.7476 (pp20) REVERT: U 110 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8238 (mm) REVERT: v 25 TYR cc_start: 0.6098 (m-80) cc_final: 0.5499 (m-80) REVERT: v 28 ARG cc_start: 0.6427 (mmt180) cc_final: 0.5658 (mmt90) REVERT: v 31 TYR cc_start: 0.6843 (t80) cc_final: 0.6601 (t80) REVERT: v 45 LEU cc_start: 0.7022 (pp) cc_final: 0.6813 (pp) REVERT: V 23 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: V 118 ARG cc_start: 0.7516 (mpt-90) cc_final: 0.7278 (mpt-90) REVERT: V 136 ARG cc_start: 0.7327 (mpp80) cc_final: 0.6786 (mtm-85) REVERT: w 143 GLU cc_start: 0.7504 (tp30) cc_final: 0.7267 (tp30) REVERT: x 42 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7271 (ttt180) REVERT: x 164 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mp) REVERT: x 263 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7081 (t-90) REVERT: 5 183 ASN cc_start: 0.8248 (m110) cc_final: 0.7841 (m110) REVERT: X 33 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: y 125 LEU cc_start: 0.8972 (tp) cc_final: 0.8713 (tp) REVERT: y 139 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: y 177 LYS cc_start: 0.7989 (tttm) cc_final: 0.7394 (ttmt) REVERT: 6 108 GLN cc_start: 0.7641 (mp10) cc_final: 0.7223 (pm20) REVERT: Y 76 GLN cc_start: 0.7808 (mt0) cc_final: 0.7573 (tt0) REVERT: z 202 ASP cc_start: 0.7960 (t0) cc_final: 0.7729 (t0) REVERT: z 298 TYR cc_start: 0.7817 (m-80) cc_final: 0.7495 (m-80) REVERT: 7 143 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7329 (m-90) REVERT: 7 163 MET cc_start: 0.6176 (ppp) cc_final: 0.5908 (ppp) REVERT: 7 222 GLU cc_start: 0.6873 (tp30) cc_final: 0.6666 (tp30) REVERT: Z 84 ASP cc_start: 0.7862 (m-30) cc_final: 0.7583 (m-30) REVERT: Z 156 GLN cc_start: 0.7361 (mm110) cc_final: 0.6835 (mm-40) REVERT: 8 121 TRP cc_start: 0.6943 (m-10) cc_final: 0.6403 (m-10) REVERT: 8 139 MET cc_start: 0.6244 (mtp) cc_final: 0.5829 (mtm) REVERT: 8 144 GLN cc_start: 0.8173 (tp40) cc_final: 0.7856 (tm-30) REVERT: b 50 GLU cc_start: 0.7669 (tp30) cc_final: 0.7363 (tp30) REVERT: d 202 MET cc_start: 0.3781 (mpp) cc_final: 0.3146 (mpp) REVERT: D 128 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7243 (tt0) REVERT: D 131 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7750 (t80) REVERT: e 70 MET cc_start: 0.5483 (mtt) cc_final: 0.5271 (tpt) REVERT: e 136 ARG cc_start: 0.5097 (mtp180) cc_final: 0.4403 (mtt-85) REVERT: e 259 GLU cc_start: 0.2896 (OUTLIER) cc_final: 0.2621 (pm20) REVERT: E 135 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (ttpp) REVERT: F 70 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6838 (mtt90) REVERT: I 65 LEU cc_start: 0.7403 (mt) cc_final: 0.7099 (mt) REVERT: i 84 LYS cc_start: 0.8451 (tttp) cc_final: 0.8159 (tttt) REVERT: L 86 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8272 (tt) REVERT: N 215 PHE cc_start: 0.8287 (t80) cc_final: 0.8084 (t80) REVERT: o 69 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: o 72 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: p 116 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7066 (mtp85) REVERT: P 134 GLN cc_start: 0.8768 (tp40) cc_final: 0.8543 (tp40) REVERT: q 44 ASP cc_start: 0.8326 (t0) cc_final: 0.7980 (t0) REVERT: s 341 MET cc_start: 0.8295 (mmm) cc_final: 0.8049 (mmm) REVERT: t 111 LYS cc_start: 0.6813 (tptp) cc_final: 0.6449 (ttpp) REVERT: t 112 GLU cc_start: 0.7507 (tt0) cc_final: 0.6672 (tt0) REVERT: t 139 ARG cc_start: 0.6799 (mmm-85) cc_final: 0.6462 (mmm-85) REVERT: t 141 ILE cc_start: 0.7848 (pt) cc_final: 0.7489 (tp) outliers start: 257 outliers final: 191 residues processed: 1400 average time/residue: 0.9418 time to fit residues: 2274.7341 Evaluate side-chains 1405 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1199 time to evaluate : 6.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain 1 residue 21 VAL Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 140 SER Chi-restraints excluded: chain x residue 164 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 312 LEU Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 336 VAL Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 259 THR Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 290 LEU Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 243 THR Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 290 ASN Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 135 THR Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 150 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 222 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 201 GLU Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 50 ARG Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 77 ASP Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 155 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 110 LYS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 72 GLU Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 149 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 120 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 657 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 chunk 634 optimal weight: 0.0370 chunk 319 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 675 optimal weight: 0.0770 chunk 723 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 834 optimal weight: 10.0000 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN Z 61 GLN d 154 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS p 176 HIS ** p 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 114085 Z= 0.195 Angle : 0.562 19.150 161589 Z= 0.273 Chirality : 0.037 0.229 19006 Planarity : 0.004 0.055 15355 Dihedral : 18.580 179.733 31788 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.96 % Rotamer: Outliers : 3.10 % Allowed : 13.90 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 9604 helix: 1.73 (0.09), residues: 3504 sheet: 0.06 (0.14), residues: 1328 loop : 0.16 (0.09), residues: 4772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 275 HIS 0.007 0.001 HIS p 176 PHE 0.022 0.001 PHE v 32 TYR 0.027 0.001 TYR z 239 ARG 0.013 0.000 ARG S 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1252 time to evaluate : 7.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 104 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7209 (mm-30) REVERT: u 108 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7145 (t0) REVERT: u 119 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6860 (mtp180) REVERT: u 144 LYS cc_start: 0.8425 (ptmm) cc_final: 0.7846 (ptpp) REVERT: u 152 LYS cc_start: 0.7089 (pttm) cc_final: 0.6674 (mttp) REVERT: U 37 GLU cc_start: 0.7825 (pp20) cc_final: 0.7516 (pp20) REVERT: U 110 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8235 (mm) REVERT: v 25 TYR cc_start: 0.6073 (m-80) cc_final: 0.5500 (m-80) REVERT: v 28 ARG cc_start: 0.6439 (mmt180) cc_final: 0.5676 (mmt90) REVERT: v 31 TYR cc_start: 0.6817 (t80) cc_final: 0.6506 (t80) REVERT: v 45 LEU cc_start: 0.6957 (pp) cc_final: 0.6736 (pp) REVERT: V 23 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: V 118 ARG cc_start: 0.7505 (mpt-90) cc_final: 0.7276 (mpt-90) REVERT: V 136 ARG cc_start: 0.7277 (mpp80) cc_final: 0.6726 (mtm-85) REVERT: w 143 GLU cc_start: 0.7523 (tp30) cc_final: 0.7319 (tp30) REVERT: x 42 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7256 (ttt180) REVERT: x 164 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7892 (mp) REVERT: x 263 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.7079 (t-90) REVERT: 5 183 ASN cc_start: 0.8229 (m110) cc_final: 0.7822 (m110) REVERT: X 33 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6597 (tt0) REVERT: X 237 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7446 (tt0) REVERT: y 125 LEU cc_start: 0.9025 (tp) cc_final: 0.8766 (tp) REVERT: y 139 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: Y 76 GLN cc_start: 0.7817 (mt0) cc_final: 0.7579 (tt0) REVERT: z 298 TYR cc_start: 0.7810 (m-80) cc_final: 0.7498 (m-80) REVERT: 7 43 MET cc_start: 0.7515 (ppp) cc_final: 0.7213 (tmm) REVERT: 7 143 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7365 (m-90) REVERT: 7 163 MET cc_start: 0.6066 (ppp) cc_final: 0.5805 (ppp) REVERT: 7 222 GLU cc_start: 0.6911 (tp30) cc_final: 0.6707 (tp30) REVERT: Z 84 ASP cc_start: 0.7851 (m-30) cc_final: 0.7568 (m-30) REVERT: Z 156 GLN cc_start: 0.7354 (mm110) cc_final: 0.6855 (mm-40) REVERT: 8 121 TRP cc_start: 0.7038 (m-10) cc_final: 0.6485 (m-10) REVERT: 8 139 MET cc_start: 0.6323 (mtp) cc_final: 0.5883 (mtm) REVERT: 8 144 GLN cc_start: 0.8128 (tp40) cc_final: 0.7833 (tm-30) REVERT: b 50 GLU cc_start: 0.7656 (tp30) cc_final: 0.7328 (tp30) REVERT: b 112 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8989 (t) REVERT: d 202 MET cc_start: 0.3783 (mpp) cc_final: 0.3176 (mpp) REVERT: D 128 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7263 (tt0) REVERT: D 131 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7810 (t80) REVERT: e 70 MET cc_start: 0.5386 (mtt) cc_final: 0.5092 (tpt) REVERT: e 222 ARG cc_start: 0.3171 (ttm170) cc_final: 0.2309 (ttp-170) REVERT: e 259 GLU cc_start: 0.2894 (OUTLIER) cc_final: 0.2626 (pm20) REVERT: F 49 ARG cc_start: 0.8202 (tmt170) cc_final: 0.7972 (tpt90) REVERT: F 70 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6837 (mtt90) REVERT: h 51 VAL cc_start: 0.7985 (t) cc_final: 0.7771 (t) REVERT: I 65 LEU cc_start: 0.7464 (mt) cc_final: 0.7177 (mt) REVERT: i 84 LYS cc_start: 0.8455 (tttp) cc_final: 0.8173 (tttt) REVERT: L 86 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8188 (tt) REVERT: M 255 MET cc_start: 0.7868 (tmm) cc_final: 0.7265 (tmm) REVERT: N 215 PHE cc_start: 0.8382 (t80) cc_final: 0.8148 (t80) REVERT: o 33 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: o 69 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: o 72 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: p 116 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7063 (mtp85) REVERT: p 181 GLU cc_start: 0.7828 (pt0) cc_final: 0.7499 (pt0) REVERT: P 134 GLN cc_start: 0.8735 (tp40) cc_final: 0.8526 (tp40) REVERT: q 44 ASP cc_start: 0.8325 (t0) cc_final: 0.7966 (t0) REVERT: r 149 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7128 (ptp-170) REVERT: s 341 MET cc_start: 0.8273 (mmm) cc_final: 0.8052 (mmm) REVERT: t 111 LYS cc_start: 0.6858 (tptp) cc_final: 0.6171 (ptmm) REVERT: t 112 GLU cc_start: 0.7599 (tt0) cc_final: 0.6555 (tt0) REVERT: t 141 ILE cc_start: 0.7874 (pt) cc_final: 0.7474 (tp) outliers start: 245 outliers final: 195 residues processed: 1393 average time/residue: 0.9525 time to fit residues: 2294.5991 Evaluate side-chains 1424 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1212 time to evaluate : 6.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 138 GLU Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 138 MET Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain 1 residue 21 VAL Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain w residue 91 ASP Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 164 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 312 LEU Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 336 VAL Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 176 LEU Chi-restraints excluded: chain y residue 259 THR Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 151 LEU Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 243 THR Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 274 VAL Chi-restraints excluded: chain z residue 290 ASN Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 150 LEU Chi-restraints excluded: chain 8 residue 184 ASN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain 9 residue 55 GLU Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 150 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 257 LEU Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 222 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 201 GLU Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 50 ARG Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 77 ASP Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 155 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 LYS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 33 GLN Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 72 GLU Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 57 THR Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 120 HIS Chi-restraints excluded: chain q residue 149 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 108 CYS Chi-restraints excluded: chain r residue 149 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 MET Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 284 VAL Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 120 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 966 optimal weight: 0.9990 chunk 1017 optimal weight: 2.9990 chunk 928 optimal weight: 2.9990 chunk 989 optimal weight: 0.0050 chunk 595 optimal weight: 8.9990 chunk 431 optimal weight: 10.0000 chunk 777 optimal weight: 0.0980 chunk 303 optimal weight: 0.2980 chunk 894 optimal weight: 40.0000 chunk 936 optimal weight: 8.9990 chunk 986 optimal weight: 7.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 358 GLN 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 229 HIS z 247 HIS 7 298 GLN Z 61 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 114085 Z= 0.132 Angle : 0.542 18.255 161589 Z= 0.261 Chirality : 0.036 0.223 19006 Planarity : 0.004 0.057 15355 Dihedral : 18.514 179.048 31788 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 2.30 % Allowed : 14.87 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 9604 helix: 1.88 (0.09), residues: 3486 sheet: 0.20 (0.14), residues: 1308 loop : 0.25 (0.09), residues: 4810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 275 HIS 0.007 0.001 HIS p 176 PHE 0.021 0.001 PHE u 140 TYR 0.018 0.001 TYR v 31 ARG 0.013 0.000 ARG S 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1288 time to evaluate : 7.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 144 LYS cc_start: 0.8336 (ptmm) cc_final: 0.7777 (ptpp) REVERT: u 152 LYS cc_start: 0.7030 (pttm) cc_final: 0.6591 (mttp) REVERT: 1 58 GLU cc_start: 0.5914 (tt0) cc_final: 0.5682 (tt0) REVERT: U 37 GLU cc_start: 0.7782 (pp20) cc_final: 0.7442 (pp20) REVERT: U 38 ASP cc_start: 0.8372 (p0) cc_final: 0.8065 (p0) REVERT: U 110 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8190 (mm) REVERT: v 25 TYR cc_start: 0.5992 (m-80) cc_final: 0.5425 (m-80) REVERT: v 31 TYR cc_start: 0.6753 (t80) cc_final: 0.6498 (t80) REVERT: v 45 LEU cc_start: 0.6848 (pp) cc_final: 0.6411 (pp) REVERT: V 118 ARG cc_start: 0.7521 (mpt-90) cc_final: 0.7315 (mpt-90) REVERT: x 164 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7898 (mp) REVERT: x 263 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: 5 183 ASN cc_start: 0.8178 (m110) cc_final: 0.7764 (m110) REVERT: X 237 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7429 (tt0) REVERT: y 125 LEU cc_start: 0.8969 (tp) cc_final: 0.8681 (tp) REVERT: y 139 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: Y 76 GLN cc_start: 0.7757 (mt0) cc_final: 0.7515 (tt0) REVERT: z 298 TYR cc_start: 0.7793 (m-80) cc_final: 0.7438 (m-80) REVERT: 7 43 MET cc_start: 0.7502 (ppp) cc_final: 0.7287 (tmm) REVERT: 7 163 MET cc_start: 0.5967 (ppp) cc_final: 0.5685 (ppp) REVERT: Z 84 ASP cc_start: 0.7794 (m-30) cc_final: 0.7575 (m-30) REVERT: Z 156 GLN cc_start: 0.7399 (mm110) cc_final: 0.6941 (mm-40) REVERT: 8 121 TRP cc_start: 0.6996 (m-10) cc_final: 0.6441 (m-10) REVERT: 8 139 MET cc_start: 0.6160 (mtp) cc_final: 0.5688 (mtm) REVERT: 8 144 GLN cc_start: 0.8086 (tp40) cc_final: 0.7790 (pp30) REVERT: 8 148 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7384 (mt-10) REVERT: d 202 MET cc_start: 0.3730 (mpp) cc_final: 0.3266 (mpp) REVERT: D 128 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7348 (tt0) REVERT: e 70 MET cc_start: 0.5549 (mtt) cc_final: 0.5231 (tpt) REVERT: e 150 ASN cc_start: 0.6707 (p0) cc_final: 0.6339 (t0) REVERT: e 222 ARG cc_start: 0.3084 (ttm170) cc_final: 0.2338 (ttp-170) REVERT: e 259 GLU cc_start: 0.2656 (OUTLIER) cc_final: 0.2275 (pm20) REVERT: F 70 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6778 (mtt90) REVERT: h 51 VAL cc_start: 0.7933 (t) cc_final: 0.7732 (t) REVERT: I 65 LEU cc_start: 0.7431 (mt) cc_final: 0.7186 (mt) REVERT: K 153 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8503 (mtpt) REVERT: L 86 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8119 (tt) REVERT: o 33 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: o 69 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: o 72 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: p 116 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7053 (mtp85) REVERT: p 181 GLU cc_start: 0.7780 (pt0) cc_final: 0.7485 (pt0) REVERT: q 44 ASP cc_start: 0.8262 (t0) cc_final: 0.7861 (t0) REVERT: t 111 LYS cc_start: 0.6948 (tptp) cc_final: 0.6262 (ptmm) REVERT: t 112 GLU cc_start: 0.7613 (tt0) cc_final: 0.6603 (tt0) REVERT: t 141 ILE cc_start: 0.7896 (pt) cc_final: 0.7507 (tp) outliers start: 182 outliers final: 139 residues processed: 1393 average time/residue: 0.9750 time to fit residues: 2347.2283 Evaluate side-chains 1359 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1210 time to evaluate : 7.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 138 MET Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain 1 residue 21 VAL Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 110 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 164 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 243 THR Chi-restraints excluded: chain z residue 247 HIS Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 201 GLU Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 LYS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 234 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 GLN Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 72 GLU Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 149 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 387 ASN Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 120 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 649 optimal weight: 0.5980 chunk 1046 optimal weight: 4.9990 chunk 638 optimal weight: 0.8980 chunk 496 optimal weight: 10.0000 chunk 727 optimal weight: 0.9990 chunk 1097 optimal weight: 20.0000 chunk 1010 optimal weight: 2.9990 chunk 874 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 675 optimal weight: 3.9990 chunk 536 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN Z 61 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS Q 212 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 114085 Z= 0.181 Angle : 0.558 18.536 161589 Z= 0.270 Chirality : 0.036 0.249 19006 Planarity : 0.004 0.070 15355 Dihedral : 18.474 178.675 31783 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 15.35 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.09), residues: 9604 helix: 1.86 (0.09), residues: 3488 sheet: 0.17 (0.14), residues: 1309 loop : 0.23 (0.09), residues: 4807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 275 HIS 0.008 0.001 HIS p 176 PHE 0.023 0.001 PHE v 32 TYR 0.019 0.001 TYR r 150 ARG 0.015 0.000 ARG S 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1226 time to evaluate : 7.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 144 LYS cc_start: 0.8317 (ptmm) cc_final: 0.7776 (ptpp) REVERT: u 152 LYS cc_start: 0.7030 (pttm) cc_final: 0.6597 (mttp) REVERT: 1 58 GLU cc_start: 0.6083 (tt0) cc_final: 0.5847 (tt0) REVERT: U 37 GLU cc_start: 0.7810 (pp20) cc_final: 0.7458 (pp20) REVERT: U 110 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mm) REVERT: v 25 TYR cc_start: 0.5954 (m-80) cc_final: 0.5422 (m-80) REVERT: v 31 TYR cc_start: 0.6766 (t80) cc_final: 0.6481 (t80) REVERT: v 45 LEU cc_start: 0.6903 (pp) cc_final: 0.6478 (pp) REVERT: V 118 ARG cc_start: 0.7506 (mpt-90) cc_final: 0.7294 (mpt-90) REVERT: x 164 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7848 (mp) REVERT: x 263 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7065 (t-90) REVERT: 5 183 ASN cc_start: 0.8300 (m110) cc_final: 0.7931 (m110) REVERT: X 53 ASN cc_start: 0.8180 (m-40) cc_final: 0.7374 (m-40) REVERT: X 237 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7458 (tt0) REVERT: y 125 LEU cc_start: 0.9010 (tp) cc_final: 0.8724 (tp) REVERT: y 139 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7532 (pp20) REVERT: Y 76 GLN cc_start: 0.7791 (mt0) cc_final: 0.7540 (tt0) REVERT: z 42 MET cc_start: 0.7609 (mmt) cc_final: 0.7403 (mmt) REVERT: z 298 TYR cc_start: 0.7793 (m-80) cc_final: 0.7439 (m-80) REVERT: 7 43 MET cc_start: 0.7511 (ppp) cc_final: 0.7270 (tmm) REVERT: 7 163 MET cc_start: 0.5994 (ppp) cc_final: 0.5763 (ppp) REVERT: Z 84 ASP cc_start: 0.7817 (m-30) cc_final: 0.7545 (m-30) REVERT: Z 156 GLN cc_start: 0.7452 (mm110) cc_final: 0.6953 (mm-40) REVERT: 8 121 TRP cc_start: 0.6992 (m-10) cc_final: 0.6388 (m-10) REVERT: 8 139 MET cc_start: 0.6376 (mtp) cc_final: 0.5908 (mtm) REVERT: 8 144 GLN cc_start: 0.8124 (tp40) cc_final: 0.7852 (tm-30) REVERT: d 202 MET cc_start: 0.3735 (mpp) cc_final: 0.3262 (mpp) REVERT: D 128 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7377 (tt0) REVERT: e 70 MET cc_start: 0.5450 (mtt) cc_final: 0.5071 (tpt) REVERT: e 222 ARG cc_start: 0.3103 (ttm170) cc_final: 0.2424 (ttp-170) REVERT: e 259 GLU cc_start: 0.2548 (OUTLIER) cc_final: 0.2283 (pm20) REVERT: F 70 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6814 (mtt90) REVERT: h 51 VAL cc_start: 0.7952 (t) cc_final: 0.7739 (t) REVERT: I 65 LEU cc_start: 0.7457 (mt) cc_final: 0.7209 (mt) REVERT: K 153 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8525 (mtpt) REVERT: L 86 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8162 (tt) REVERT: M 255 MET cc_start: 0.7875 (tmm) cc_final: 0.7147 (tmm) REVERT: o 33 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: o 69 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: o 72 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: p 116 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7057 (mtp85) REVERT: p 181 GLU cc_start: 0.7809 (pt0) cc_final: 0.7493 (pt0) REVERT: q 44 ASP cc_start: 0.8288 (t0) cc_final: 0.7895 (t0) REVERT: t 111 LYS cc_start: 0.6919 (tptp) cc_final: 0.6266 (ptmm) REVERT: t 112 GLU cc_start: 0.7684 (tt0) cc_final: 0.6696 (tt0) REVERT: t 141 ILE cc_start: 0.7987 (pt) cc_final: 0.7573 (tp) outliers start: 173 outliers final: 149 residues processed: 1329 average time/residue: 1.0017 time to fit residues: 2298.1863 Evaluate side-chains 1373 residues out of total 8568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1214 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain u residue 108 ASP Chi-restraints excluded: chain u residue 128 SER Chi-restraints excluded: chain u residue 138 MET Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain 1 residue 21 VAL Chi-restraints excluded: chain U residue 27 GLN Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 110 LEU Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 69 ILE Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain x residue 50 MET Chi-restraints excluded: chain x residue 164 LEU Chi-restraints excluded: chain x residue 221 VAL Chi-restraints excluded: chain x residue 263 HIS Chi-restraints excluded: chain x residue 315 LEU Chi-restraints excluded: chain x residue 319 TYR Chi-restraints excluded: chain x residue 368 LEU Chi-restraints excluded: chain 5 residue 207 SER Chi-restraints excluded: chain 5 residue 220 LEU Chi-restraints excluded: chain 5 residue 256 PHE Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 331 ASN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 231 VAL Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 127 ILE Chi-restraints excluded: chain y residue 139 GLU Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 308 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 275 GLN Chi-restraints excluded: chain z residue 76 LYS Chi-restraints excluded: chain z residue 105 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 114 VAL Chi-restraints excluded: chain z residue 228 ASP Chi-restraints excluded: chain z residue 243 THR Chi-restraints excluded: chain z residue 253 VAL Chi-restraints excluded: chain z residue 291 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 97 GLU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 253 LYS Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 91 LEU Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 159 LEU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 201 GLU Chi-restraints excluded: chain e residue 223 THR Chi-restraints excluded: chain e residue 259 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain f residue 101 THR Chi-restraints excluded: chain f residue 114 CYS Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 205 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain g residue 37 ARG Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 110 LYS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 234 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 GLN Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 72 GLU Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 111 ILE Chi-restraints excluded: chain p residue 116 ARG Chi-restraints excluded: chain p residue 157 MET Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 149 ASP Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 263 THR Chi-restraints excluded: chain s residue 405 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain t residue 87 ASP Chi-restraints excluded: chain t residue 94 VAL Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 118 VAL Chi-restraints excluded: chain t residue 120 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 694 optimal weight: 7.9990 chunk 931 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 806 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 875 optimal weight: 8.9990 chunk 366 optimal weight: 0.9990 chunk 899 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 161 optimal weight: 0.0670 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN V 78 GLN ** V 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 218 HIS 5 206 ASN 5 324 GLN 5 384 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 189 HIS 7 298 GLN Z 61 GLN f 153 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100165 restraints weight = 245627.909| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.01 r_work: 0.3334 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 114085 Z= 0.241 Angle : 0.592 19.162 161589 Z= 0.288 Chirality : 0.038 0.293 19006 Planarity : 0.004 0.061 15355 Dihedral : 18.524 179.181 31783 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 15.16 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.01 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 9604 helix: 1.71 (0.09), residues: 3494 sheet: 0.01 (0.14), residues: 1329 loop : 0.16 (0.09), residues: 4781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 275 HIS 0.008 0.001 HIS p 176 PHE 0.022 0.001 PHE u 124 TYR 0.023 0.001 TYR r 150 ARG 0.015 0.000 ARG S 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35020.83 seconds wall clock time: 607 minutes 45.72 seconds (36465.72 seconds total)