Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 08:20:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r84_4751/07_2023/6r84_4751_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Se 1 7.20 5 Zn 1 6.06 5 P 3671 5.49 5 S 138 5.16 5 C 73214 2.51 5 N 25487 2.21 5 O 36292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 108": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "R ARG 443": "NH1" <-> "NH2" Residue "R ARG 461": "NH1" <-> "NH2" Residue "R ARG 503": "NH1" <-> "NH2" Residue "R ARG 506": "NH1" <-> "NH2" Residue "R ARG 513": "NH1" <-> "NH2" Residue "R ARG 518": "NH1" <-> "NH2" Residue "R ARG 525": "NH1" <-> "NH2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "j ARG 105": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "7 ARG 23": "NH1" <-> "NH2" Residue "7 ARG 91": "NH1" <-> "NH2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "5 ARG 3": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 126": "NH1" <-> "NH2" Residue "5 ARG 128": "NH1" <-> "NH2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 ARG 181": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 176": "NH1" <-> "NH2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s ARG 152": "NH1" <-> "NH2" Residue "s ARG 153": "NH1" <-> "NH2" Residue "s ARG 177": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 139": "NH1" <-> "NH2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "Z ARG 125": "NH1" <-> "NH2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "a ARG 121": "NH1" <-> "NH2" Residue "b ARG 84": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "e PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "f ARG 70": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "h TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 138804 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3522 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 433} Chain breaks: 3 Chain: "R" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2804 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 11, 'TRANS': 348} Chain breaks: 10 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'UNK:plan-1': 44} Unresolved non-hydrogen planarities: 44 Chain: "X" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1633 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "i" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "j" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "K" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "7" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "l" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "M" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "m" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "n" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "o" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "p" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Q" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "5" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "s" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1228 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain: "U" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "V" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "W" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 737 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 180 Chain: "r" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "x" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 59, 'rna3p_pyr': 57} Link IDs: {'rna2p': 5, 'rna3p': 115} Chain: "Y" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 513 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 70, 'rna3p_pyr': 75} Link IDs: {'rna2p': 13, 'rna3p': 144} Chain: "Z" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 60} Chain: "b" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "c" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "E" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "F" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "h" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "1" Number of atoms: 70924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3316, 70924 Classifications: {'RNA': 3316} Modifications used: {'rna2p_pur': 198, 'rna2p_pyr': 125, 'rna3p_pur': 1633, 'rna3p_pyr': 1360} Link IDs: {'rna2p': 323, 'rna3p': 2992} Chain breaks: 4 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3737 SG CYS R 77 37.539 89.629 115.260 1.00150.54 S Time building chain proxies: 46.58, per 1000 atoms: 0.34 Number of scatterers: 138804 At special positions: 0 Unit cell: (236.312, 214.632, 275.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 1 33.99 Zn 1 29.99 S 138 16.00 P 3671 15.00 O 36292 8.00 N 25487 7.00 C 73214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.84 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 601 " pdb="ZN ZN R 601 " - pdb=" ND1 HIS R 96 " pdb="ZN ZN R 601 " - pdb=" SG CYS R 77 " 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14336 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 75 sheets defined 35.0% alpha, 13.2% beta 1133 base pairs and 1951 stacking pairs defined. Time for finding SS restraints: 40.41 Creating SS restraints... Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.680A pdb=" N ASP A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.197A pdb=" N ILE A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.656A pdb=" N CYS A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.687A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 343 Processing helix chain 'A' and resid 346 through 367 removed outlier: 3.627A pdb=" N VAL A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.576A pdb=" N SER A 467 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN A 468 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.831A pdb=" N GLN A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 510 removed outlier: 4.033A pdb=" N THR A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 542 through 545 removed outlier: 4.497A pdb=" N GLY A 545 " --> pdb=" O PRO A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'R' and resid 15 through 23 removed outlier: 3.930A pdb=" N TYR R 19 " --> pdb=" O ASN R 16 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE R 20 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE R 21 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU R 23 " --> pdb=" O ILE R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 Processing helix chain 'R' and resid 93 through 105 Processing helix chain 'R' and resid 114 through 123 removed outlier: 3.521A pdb=" N UNK R 123 " --> pdb=" O UNK R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 173 Processing helix chain 'R' and resid 218 through 227 removed outlier: 4.404A pdb=" N ALA R 222 " --> pdb=" O ASN R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 311 through 331 Processing helix chain 'R' and resid 331 through 337 Processing helix chain 'R' and resid 347 through 354 removed outlier: 3.767A pdb=" N PHE R 354 " --> pdb=" O ASP R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 390 Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'R' and resid 445 through 454 Processing helix chain 'R' and resid 459 through 463 removed outlier: 3.538A pdb=" N LYS R 463 " --> pdb=" O PHE R 460 " (cutoff:3.500A) Processing helix chain 'R' and resid 473 through 482 removed outlier: 3.517A pdb=" N TYR R 477 " --> pdb=" O THR R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 483 through 493 Processing helix chain 'R' and resid 507 through 515 Processing helix chain 'R' and resid 517 through 527 removed outlier: 3.513A pdb=" N PHE R 521 " --> pdb=" O VAL R 517 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN R 527 " --> pdb=" O ILE R 523 " (cutoff:3.500A) Processing helix chain 'R' and resid 536 through 549 Processing helix chain 'X' and resid 12 through 16 removed outlier: 4.320A pdb=" N PHE X 16 " --> pdb=" O GLU X 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 12 through 16' Processing helix chain 'X' and resid 31 through 42 removed outlier: 3.783A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 77 through 88 Processing helix chain 'X' and resid 103 through 108 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 166 through 177 Processing helix chain 'X' and resid 211 through 222 removed outlier: 3.599A pdb=" N VAL X 217 " --> pdb=" O PRO X 213 " (cutoff:3.500A) Processing helix chain 'i' and resid 60 through 65 removed outlier: 3.564A pdb=" N VAL i 65 " --> pdb=" O TYR i 62 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 71 removed outlier: 3.940A pdb=" N LYS i 70 " --> pdb=" O SER i 66 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 105 removed outlier: 4.072A pdb=" N ALA i 92 " --> pdb=" O ARG i 88 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU i 96 " --> pdb=" O ALA i 92 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 72 Processing helix chain 'J' and resid 96 through 106 Processing helix chain 'J' and resid 120 through 130 Processing helix chain 'J' and resid 140 through 151 removed outlier: 3.803A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.326A pdb=" N ILE J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 190 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 235 through 244 removed outlier: 3.592A pdb=" N SER J 242 " --> pdb=" O LYS J 238 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 34 removed outlier: 3.622A pdb=" N SER j 19 " --> pdb=" O GLU j 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 43 No H-bonds generated for 'chain 'j' and resid 41 through 43' Processing helix chain 'j' and resid 44 through 70 removed outlier: 4.495A pdb=" N SER j 50 " --> pdb=" O THR j 46 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN j 59 " --> pdb=" O LEU j 55 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA j 65 " --> pdb=" O GLN j 61 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL j 66 " --> pdb=" O GLN j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 81 removed outlier: 3.623A pdb=" N ARG j 81 " --> pdb=" O LYS j 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 99 Processing helix chain 'j' and resid 101 through 111 Processing helix chain 'K' and resid 53 through 69 Processing helix chain 'K' and resid 83 through 97 Processing helix chain 'K' and resid 101 through 119 Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 159 through 163 Processing helix chain 'K' and resid 165 through 173 Processing helix chain 'K' and resid 182 through 189 removed outlier: 4.191A pdb=" N LEU K 186 " --> pdb=" O GLY K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 222 Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.543A pdb=" N VAL K 229 " --> pdb=" O LYS K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 254 removed outlier: 3.688A pdb=" N ASP K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 49 Processing helix chain 'k' and resid 51 through 63 removed outlier: 4.046A pdb=" N ARG k 62 " --> pdb=" O ILE k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 64 through 76 removed outlier: 4.077A pdb=" N ARG k 68 " --> pdb=" O SER k 64 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 98 removed outlier: 4.105A pdb=" N ALA k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER k 97 " --> pdb=" O ILE k 93 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 84 Processing helix chain '7' and resid 150 through 163 Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'l' and resid 50 through 58 removed outlier: 3.548A pdb=" N LYS l 54 " --> pdb=" O GLY l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 69 Processing helix chain 'l' and resid 70 through 76 removed outlier: 3.662A pdb=" N ASN l 76 " --> pdb=" O ARG l 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 42 Processing helix chain 'M' and resid 72 through 87 removed outlier: 4.011A pdb=" N ALA M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 removed outlier: 3.757A pdb=" N LEU M 112 " --> pdb=" O HIS M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.666A pdb=" N LYS M 166 " --> pdb=" O TRP M 162 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 16 Processing helix chain 'm' and resid 58 through 68 removed outlier: 4.474A pdb=" N LYS m 64 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN m 67 " --> pdb=" O LYS m 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 20 Processing helix chain 'N' and resid 27 through 46 removed outlier: 3.911A pdb=" N ALA N 43 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 3.796A pdb=" N VAL N 80 " --> pdb=" O THR N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 105 through 122 Processing helix chain 'N' and resid 166 through 179 removed outlier: 4.123A pdb=" N GLU N 176 " --> pdb=" O LEU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 192 removed outlier: 3.625A pdb=" N ALA N 187 " --> pdb=" O ARG N 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 19 Processing helix chain 'n' and resid 24 through 29 removed outlier: 4.377A pdb=" N ARG n 28 " --> pdb=" O PRO n 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU n 29 " --> pdb=" O GLN n 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 24 through 29' Processing helix chain 'O' and resid 77 through 89 Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 3.500A pdb=" N LYS O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 135 Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.960A pdb=" N LEU o 85 " --> pdb=" O SER o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 13 removed outlier: 3.606A pdb=" N LYS p 13 " --> pdb=" O GLU p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 32 Processing helix chain 'p' and resid 44 through 50 removed outlier: 3.518A pdb=" N ARG p 50 " --> pdb=" O ASP p 46 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 79 removed outlier: 3.705A pdb=" N GLY p 78 " --> pdb=" O VAL p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 110 Processing helix chain 'p' and resid 139 through 144 Processing helix chain 'p' and resid 153 through 157 removed outlier: 3.993A pdb=" N LYS p 157 " --> pdb=" O PRO p 154 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 188 through 193 Processing helix chain 'Q' and resid 15 through 28 removed outlier: 3.792A pdb=" N VAL Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 40 removed outlier: 4.005A pdb=" N GLU Q 40 " --> pdb=" O ARG Q 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 37 through 40' Processing helix chain 'Q' and resid 46 through 58 removed outlier: 3.915A pdb=" N PHE Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 100 removed outlier: 3.524A pdb=" N LYS Q 96 " --> pdb=" O THR Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 146 Processing helix chain 'Q' and resid 149 through 185 removed outlier: 4.621A pdb=" N VAL Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE Q 174 " --> pdb=" O LYS Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 197 Processing helix chain '5' and resid 28 through 36 Processing helix chain '5' and resid 40 through 52 removed outlier: 3.785A pdb=" N GLU 5 49 " --> pdb=" O GLN 5 45 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN 5 50 " --> pdb=" O LYS 5 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL 5 51 " --> pdb=" O TYR 5 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 5 52 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 76 Processing helix chain '5' and resid 84 through 105 removed outlier: 4.199A pdb=" N LEU 5 94 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS 5 105 " --> pdb=" O ASN 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 108 through 110 No H-bonds generated for 'chain '5' and resid 108 through 110' Processing helix chain '5' and resid 131 through 135 removed outlier: 3.857A pdb=" N GLY 5 134 " --> pdb=" O ARG 5 131 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 5 135 " --> pdb=" O ALA 5 132 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 131 through 135' Processing helix chain '5' and resid 169 through 177 Processing helix chain 'S' and resid 23 through 40 removed outlier: 4.059A pdb=" N PHE S 35 " --> pdb=" O LYS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 52 removed outlier: 3.527A pdb=" N VAL S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU S 49 " --> pdb=" O ASN S 45 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 72 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 124 through 131 Processing helix chain 'S' and resid 149 through 153 removed outlier: 3.596A pdb=" N PHE S 153 " --> pdb=" O VAL S 150 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 61 through 77 removed outlier: 3.711A pdb=" N MET s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 83 removed outlier: 4.034A pdb=" N ALA s 83 " --> pdb=" O GLY s 80 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 80 through 83' Processing helix chain 's' and resid 140 through 142 No H-bonds generated for 'chain 's' and resid 140 through 142' Processing helix chain 's' and resid 143 through 153 removed outlier: 3.560A pdb=" N VAL s 148 " --> pdb=" O LYS s 144 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU s 149 " --> pdb=" O ASP s 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG s 153 " --> pdb=" O GLU s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 154 through 158 removed outlier: 3.690A pdb=" N PHE s 158 " --> pdb=" O ARG s 155 " (cutoff:3.500A) Processing helix chain 's' and resid 169 through 173 removed outlier: 4.544A pdb=" N PHE s 172 " --> pdb=" O LYS s 169 " (cutoff:3.500A) Processing helix chain 's' and resid 176 through 187 removed outlier: 3.599A pdb=" N GLU s 185 " --> pdb=" O LEU s 181 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 212 removed outlier: 3.608A pdb=" N ASN s 208 " --> pdb=" O SER s 204 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 28 through 33 Processing helix chain 'T' and resid 37 through 47 removed outlier: 3.771A pdb=" N LYS T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 72 Processing helix chain 'T' and resid 84 through 89 removed outlier: 4.026A pdb=" N LEU T 89 " --> pdb=" O ARG T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 112 Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.788A pdb=" N LYS T 125 " --> pdb=" O HIS T 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY T 129 " --> pdb=" O LYS T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 152 Processing helix chain 'U' and resid 33 through 47 removed outlier: 3.756A pdb=" N LYS U 47 " --> pdb=" O TYR U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 111 Processing helix chain 'U' and resid 137 through 142 removed outlier: 3.745A pdb=" N LYS U 141 " --> pdb=" O ARG U 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 58 Processing helix chain 'V' and resid 99 through 123 removed outlier: 4.166A pdb=" N GLN V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA V 121 " --> pdb=" O ALA V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 24 removed outlier: 3.796A pdb=" N THR W 23 " --> pdb=" O VAL W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 38 Processing helix chain 'W' and resid 72 through 87 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.825A pdb=" N LYS P 31 " --> pdb=" O LEU P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 47 removed outlier: 3.530A pdb=" N GLU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA P 47 " --> pdb=" O GLY P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 84 Processing helix chain 'P' and resid 108 through 113 removed outlier: 3.554A pdb=" N ALA P 113 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 133 removed outlier: 3.530A pdb=" N GLU P 131 " --> pdb=" O SER P 127 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 22 removed outlier: 3.855A pdb=" N TYR r 22 " --> pdb=" O TYR r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.832A pdb=" N GLU r 40 " --> pdb=" O GLN r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 65 removed outlier: 3.958A pdb=" N ARG r 61 " --> pdb=" O THR r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 80 removed outlier: 4.073A pdb=" N LYS r 75 " --> pdb=" O ASP r 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU r 76 " --> pdb=" O PHE r 73 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU r 77 " --> pdb=" O GLU r 74 " (cutoff:3.500A) Proline residue: r 78 - end of helix Processing helix chain 'r' and resid 93 through 103 removed outlier: 3.740A pdb=" N LYS r 97 " --> pdb=" O LEU r 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER r 102 " --> pdb=" O ASN r 98 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN r 103 " --> pdb=" O VAL r 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 119 through 124 Processing helix chain 'x' and resid 126 through 133 Processing helix chain 'Y' and resid 33 through 41 removed outlier: 3.907A pdb=" N ALA Y 37 " --> pdb=" O ASN Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 49 removed outlier: 3.568A pdb=" N ILE Y 49 " --> pdb=" O PRO Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 59 removed outlier: 3.512A pdb=" N HIS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 62 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 91 through 103 removed outlier: 3.546A pdb=" N LYS Z 96 " --> pdb=" O LYS Z 92 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Z 100 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 140 removed outlier: 4.649A pdb=" N ARG Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 21 Processing helix chain 'a' and resid 23 through 31 removed outlier: 4.480A pdb=" N VAL a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 44 Processing helix chain 'a' and resid 113 through 121 Processing helix chain 'b' and resid 58 through 64 Processing helix chain 'b' and resid 104 through 123 removed outlier: 3.985A pdb=" N GLU b 108 " --> pdb=" O PRO b 104 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 48 Processing helix chain 'c' and resid 6 through 11 removed outlier: 4.009A pdb=" N LYS c 10 " --> pdb=" O THR c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 46 Processing helix chain 'c' and resid 64 through 69 removed outlier: 3.672A pdb=" N TRP c 69 " --> pdb=" O ALA c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 3.876A pdb=" N ASP c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN c 89 " --> pdb=" O ASP c 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 108 Processing helix chain 'c' and resid 131 through 141 removed outlier: 3.684A pdb=" N LYS c 137 " --> pdb=" O LEU c 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.721A pdb=" N THR D 11 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 removed outlier: 3.635A pdb=" N LEU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.871A pdb=" N THR D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 Processing helix chain 'd' and resid 36 through 56 Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 173 through 177 removed outlier: 3.906A pdb=" N LYS E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.858A pdb=" N ALA E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 19 Processing helix chain 'e' and resid 26 through 36 removed outlier: 3.640A pdb=" N GLN e 36 " --> pdb=" O LYS e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 64 removed outlier: 3.705A pdb=" N LEU e 62 " --> pdb=" O TYR e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.959A pdb=" N PHE F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 165 through 169 removed outlier: 3.584A pdb=" N THR F 169 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'f' and resid 24 through 26 No H-bonds generated for 'chain 'f' and resid 24 through 26' Processing helix chain 'f' and resid 27 through 45 removed outlier: 3.511A pdb=" N ARG f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS f 38 " --> pdb=" O LYS f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 60 Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 132 through 138 Processing helix chain 'G' and resid 153 through 159 removed outlier: 3.700A pdb=" N LEU G 156 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 173 removed outlier: 3.858A pdb=" N ALA G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 179 Processing helix chain 'G' and resid 190 through 195 removed outlier: 3.763A pdb=" N LYS G 193 " --> pdb=" O GLY G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 Processing helix chain 'G' and resid 234 through 239 Processing helix chain 'G' and resid 240 through 243 Processing helix chain 'G' and resid 252 through 263 Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 320 through 327 removed outlier: 3.775A pdb=" N LEU G 327 " --> pdb=" O VAL G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 335 removed outlier: 3.966A pdb=" N VAL G 333 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 360 removed outlier: 3.543A pdb=" N THR G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 58 Processing helix chain 'g' and resid 78 through 83 Processing helix chain 'g' and resid 84 through 86 No H-bonds generated for 'chain 'g' and resid 84 through 86' Processing helix chain 'g' and resid 101 through 116 removed outlier: 3.503A pdb=" N ARG g 105 " --> pdb=" O SER g 101 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.188A pdb=" N ARG H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 94 through 113 Processing helix chain 'H' and resid 157 through 169 Processing helix chain 'H' and resid 176 through 180 removed outlier: 4.278A pdb=" N ARG H 179 " --> pdb=" O SER H 176 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE H 180 " --> pdb=" O GLU H 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 176 through 180' Processing helix chain 'H' and resid 191 through 200 removed outlier: 3.524A pdb=" N LEU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.829A pdb=" N SER H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 222 removed outlier: 3.810A pdb=" N PHE H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'H' and resid 234 through 250 removed outlier: 4.141A pdb=" N ASP H 238 " --> pdb=" O ASP H 234 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 243 " --> pdb=" O ILE H 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 270 removed outlier: 3.968A pdb=" N TYR H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 293 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.958A pdb=" N LYS I 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.780A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 160 removed outlier: 3.566A pdb=" N SER I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 147 removed outlier: 3.531A pdb=" N GLY L 146 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 186 removed outlier: 3.623A pdb=" N ILE L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER L 186 " --> pdb=" O GLN L 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 251 removed outlier: 6.184A pdb=" N LEU A 248 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL A 279 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 250 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG A 109 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 294 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 111 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET A 296 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 113 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 418 removed outlier: 3.566A pdb=" N HIS A 413 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE A 398 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN A 415 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP A 396 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLY A 417 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA A 394 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 398 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 449 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 462 removed outlier: 6.712A pdb=" N GLY A 461 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP A 540 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 537 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 568 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 539 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 424 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 190 through 193 Processing sheet with id=AA5, first strand: chain 'R' and resid 276 through 282 removed outlier: 6.378A pdb=" N PHE R 276 " --> pdb=" O SER R 252 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER R 252 " --> pdb=" O PHE R 276 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE R 235 " --> pdb=" O ASN R 340 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE R 342 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA R 237 " --> pdb=" O PHE R 342 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG R 344 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE R 239 " --> pdb=" O ARG R 344 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N LYS R 368 " --> pdb=" O ASP R 339 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE R 341 " --> pdb=" O LYS R 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'X' and resid 17 through 19 removed outlier: 6.615A pdb=" N CYS X 24 " --> pdb=" O VAL X 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 64 through 65 removed outlier: 3.522A pdb=" N ALA X 64 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN X 95 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 114 through 117 removed outlier: 6.070A pdb=" N ALA X 115 " --> pdb=" O PHE X 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'X' and resid 153 through 154 removed outlier: 6.939A pdb=" N GLY X 159 " --> pdb=" O VAL X 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'i' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'J' and resid 205 through 206 removed outlier: 4.176A pdb=" N SER J 113 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'j' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 179 Processing sheet with id=AB7, first strand: chain '7' and resid 3 through 11 removed outlier: 6.645A pdb=" N ILE 7 4 " --> pdb=" O ASN 7 59 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 7 52 " --> pdb=" O VAL 7 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 17 through 20 Processing sheet with id=AB9, first strand: chain '7' and resid 133 through 136 removed outlier: 6.511A pdb=" N LYS 7 87 " --> pdb=" O LYS 7 184 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS 7 184 " --> pdb=" O LYS 7 87 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS 7 89 " --> pdb=" O SER 7 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR 7 180 " --> pdb=" O ARG 7 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '7' and resid 100 through 104 Processing sheet with id=AC2, first strand: chain 'l' and resid 16 through 17 removed outlier: 3.581A pdb=" N THR l 33 " --> pdb=" O HIS l 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 46 through 48 removed outlier: 7.144A pdb=" N VAL M 130 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU M 17 " --> pdb=" O TYR M 128 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR M 128 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU M 19 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP M 126 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'm' and resid 51 through 56 removed outlier: 4.704A pdb=" N THR m 22 " --> pdb=" O ARG m 46 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA m 23 " --> pdb=" O ASN m 76 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 22 through 23 Processing sheet with id=AC6, first strand: chain 'N' and resid 57 through 59 Processing sheet with id=AC7, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.503A pdb=" N ARG N 157 " --> pdb=" O ALA c 99 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL c 125 " --> pdb=" O GLU c 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 53 through 59 removed outlier: 4.990A pdb=" N GLY O 48 " --> pdb=" O PRO O 54 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL O 20 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 102 through 103 Processing sheet with id=AD1, first strand: chain 'p' and resid 36 through 39 removed outlier: 3.916A pdb=" N ILE p 61 " --> pdb=" O ALA p 39 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU p 131 " --> pdb=" O TRP p 120 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TRP p 120 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.090A pdb=" N VAL Q 7 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL Q 36 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE Q 9 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 42 through 44 Processing sheet with id=AD4, first strand: chain '5' and resid 14 through 17 removed outlier: 6.172A pdb=" N HIS 5 145 " --> pdb=" O VAL 5 119 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL 5 119 " --> pdb=" O HIS 5 145 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU 5 147 " --> pdb=" O ILE 5 117 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE 5 117 " --> pdb=" O GLU 5 147 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL 5 149 " --> pdb=" O SER 5 115 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '5' and resid 58 through 59 Processing sheet with id=AD6, first strand: chain '5' and resid 127 through 128 Processing sheet with id=AD7, first strand: chain 'S' and resid 62 through 63 removed outlier: 6.455A pdb=" N VAL S 62 " --> pdb=" O THR S 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'S' and resid 121 through 123 removed outlier: 6.090A pdb=" N VAL S 81 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 's' and resid 34 through 36 Processing sheet with id=AE1, first strand: chain 's' and resid 133 through 136 removed outlier: 4.211A pdb=" N PHE s 135 " --> pdb=" O LEU s 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 57 through 60 removed outlier: 6.731A pdb=" N LEU s 96 " --> pdb=" O HIS s 122 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU s 124 " --> pdb=" O HIS s 94 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS s 94 " --> pdb=" O LEU s 124 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 189 through 191 Processing sheet with id=AE4, first strand: chain 'U' and resid 60 through 64 removed outlier: 3.644A pdb=" N GLY U 11 " --> pdb=" O PHE U 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 88 through 96 removed outlier: 6.807A pdb=" N ASN U 74 " --> pdb=" O GLU U 128 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU U 128 " --> pdb=" O ASN U 74 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY U 76 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL U 126 " --> pdb=" O GLY U 76 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TRP U 78 " --> pdb=" O LEU U 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 84 through 92 removed outlier: 3.554A pdb=" N ASN V 66 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE V 75 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL V 64 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASN V 77 " --> pdb=" O GLY V 62 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 54 through 57 removed outlier: 7.748A pdb=" N TYR W 103 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR W 16 " --> pdb=" O TYR W 103 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AE9, first strand: chain 'r' and resid 50 through 52 removed outlier: 3.696A pdb=" N VAL r 190 " --> pdb=" O PHE r 197 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'x' and resid 34 through 39 removed outlier: 6.849A pdb=" N MET x 59 " --> pdb=" O ILE x 37 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL x 39 " --> pdb=" O MET x 57 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N MET x 57 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'x' and resid 85 through 86 Processing sheet with id=AF3, first strand: chain 'x' and resid 117 through 118 Processing sheet with id=AF4, first strand: chain 'Y' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'Z' and resid 63 through 66 removed outlier: 3.513A pdb=" N GLN Z 65 " --> pdb=" O GLN Z 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG Z 125 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS Z 109 " --> pdb=" O ARG Z 125 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 33 through 34 Processing sheet with id=AF7, first strand: chain 'a' and resid 94 through 99 removed outlier: 3.640A pdb=" N ILE a 97 " --> pdb=" O VAL a 85 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL a 85 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N LEU a 99 " --> pdb=" O ASP a 83 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N ASP a 83 " --> pdb=" O LEU a 99 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA a 79 " --> pdb=" O VAL a 73 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL a 73 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN a 81 " --> pdb=" O SER a 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS a 69 " --> pdb=" O ASP a 83 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL a 85 " --> pdb=" O GLU a 67 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU a 67 " --> pdb=" O VAL a 85 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU a 55 " --> pdb=" O THR a 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 69 through 76 removed outlier: 6.494A pdb=" N LYS b 69 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA b 44 " --> pdb=" O ILE b 25 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE b 25 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE b 46 " --> pdb=" O VAL b 23 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL b 23 " --> pdb=" O ILE b 46 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ARG b 48 " --> pdb=" O LYS b 21 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N LYS b 21 " --> pdb=" O ARG b 48 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS b 21 " --> pdb=" O VAL b 13 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS b 9 " --> pdb=" O ILE b 25 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL b 10 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 7 through 12 removed outlier: 3.600A pdb=" N LYS C 19 " --> pdb=" O CYS C 12 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG C 87 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL C 68 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 72 through 73 Processing sheet with id=AG2, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AG3, first strand: chain 'E' and resid 71 through 77 removed outlier: 3.568A pdb=" N GLN E 47 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL E 62 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL E 45 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 64 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY E 43 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 101 through 103 removed outlier: 6.435A pdb=" N ARG E 147 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N HIS E 139 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS E 145 " --> pdb=" O HIS E 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AG6, first strand: chain 'e' and resid 22 through 25 removed outlier: 6.639A pdb=" N LYS e 22 " --> pdb=" O LEU e 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE e 42 " --> pdb=" O TYR e 68 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 356 through 359 removed outlier: 7.346A pdb=" N LEU F 356 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP F 59 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE F 335 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL F 220 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA F 217 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE F 278 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA F 219 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR F 276 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE F 282 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS F 325 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG F 70 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP F 59 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL F 72 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL F 57 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU F 74 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR F 55 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL F 76 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL F 78 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 98 through 106 removed outlier: 5.135A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR F 95 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER F 101 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL F 93 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR F 103 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL F 86 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS F 163 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL F 157 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 98 through 106 removed outlier: 5.135A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR F 95 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER F 101 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL F 93 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR F 103 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 223 through 227 Processing sheet with id=AH2, first strand: chain 'f' and resid 49 through 51 removed outlier: 6.791A pdb=" N ARG f 50 " --> pdb=" O VAL f 93 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 6 through 10 removed outlier: 5.760A pdb=" N ASN G 18 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER G 10 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR G 16 " --> pdb=" O SER G 10 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 150 through 152 removed outlier: 4.511A pdb=" N LEU G 150 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU G 206 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR G 251 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL G 208 " --> pdb=" O THR G 251 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 186 through 187 Processing sheet with id=AH6, first strand: chain 'g' and resid 72 through 76 Processing sheet with id=AH7, first strand: chain 'H' and resid 73 through 79 removed outlier: 6.713A pdb=" N ILE H 64 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA H 77 " --> pdb=" O CYS H 62 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS H 62 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR H 79 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 60 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 8 through 14 removed outlier: 4.488A pdb=" N LEU h 29 " --> pdb=" O LEU h 14 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL h 80 " --> pdb=" O THR h 74 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR h 74 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG h 82 " --> pdb=" O THR h 72 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG h 48 " --> pdb=" O PHE h 101 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL h 52 " --> pdb=" O SER h 97 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER h 97 " --> pdb=" O VAL h 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'h' and resid 17 through 18 removed outlier: 3.697A pdb=" N GLN h 17 " --> pdb=" O ASN h 24 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 77 through 80 removed outlier: 7.191A pdb=" N THR I 62 " --> pdb=" O HIS I 57 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS I 57 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU I 64 " --> pdb=" O LEU I 55 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR I 38 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL I 39 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AI3, first strand: chain 'L' and resid 205 through 206 2050 hydrogen bonds defined for protein. 5799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2789 hydrogen bonds 4474 hydrogen bond angles 0 basepair planarities 1133 basepair parallelities 1951 stacking parallelities Total time for adding SS restraints: 245.62 Time building geometry restraints manager: 57.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 13382 1.29 - 1.46: 73182 1.46 - 1.62: 62388 1.62 - 1.79: 92 1.79 - 1.95: 150 Bond restraints: 149194 Sorted by residual: bond pdb=" C LYS F 237 " pdb=" N LEU F 238 " ideal model delta sigma weight residual 1.331 1.131 0.201 1.54e-02 4.22e+03 1.70e+02 bond pdb=" C PRO A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.01e-02 9.80e+03 2.15e+01 bond pdb=" C LYS 7 122 " pdb=" N ILE 7 123 " ideal model delta sigma weight residual 1.332 1.297 0.035 9.20e-03 1.18e+04 1.41e+01 bond pdb=" C ALA a 47 " pdb=" N LEU a 48 " ideal model delta sigma weight residual 1.325 1.279 0.046 1.24e-02 6.50e+03 1.38e+01 bond pdb=" CA PHE F 16 " pdb=" CB PHE F 16 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.49e-02 4.50e+03 9.89e+00 ... (remaining 149189 not shown) Histogram of bond angle deviations from ideal: 94.40 - 103.51: 10172 103.51 - 112.63: 92194 112.63 - 121.74: 82026 121.74 - 130.85: 33461 130.85 - 139.97: 1532 Bond angle restraints: 219385 Sorted by residual: angle pdb=" C PRO N 48 " pdb=" N ARG N 49 " pdb=" CA ARG N 49 " ideal model delta sigma weight residual 121.48 139.97 -18.49 2.04e+00 2.40e-01 8.21e+01 angle pdb=" N VAL L 191 " pdb=" CA VAL L 191 " pdb=" C VAL L 191 " ideal model delta sigma weight residual 112.83 106.31 6.52 9.90e-01 1.02e+00 4.34e+01 angle pdb=" C PRO N 61 " pdb=" N THR N 62 " pdb=" CA THR N 62 " ideal model delta sigma weight residual 121.54 133.99 -12.45 1.91e+00 2.74e-01 4.25e+01 angle pdb=" C LYS i 24 " pdb=" N THR i 25 " pdb=" CA THR i 25 " ideal model delta sigma weight residual 122.29 131.90 -9.61 1.48e+00 4.57e-01 4.21e+01 angle pdb=" C VAL 5 157 " pdb=" N ALA 5 158 " pdb=" CA ALA 5 158 " ideal model delta sigma weight residual 121.31 130.98 -9.67 1.49e+00 4.50e-01 4.21e+01 ... (remaining 219380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 78135 35.80 - 71.59: 3213 71.59 - 107.39: 250 107.39 - 143.19: 54 143.19 - 178.98: 97 Dihedral angle restraints: 81749 sinusoidal: 59536 harmonic: 22213 Sorted by residual: dihedral pdb=" CA ASN J 157 " pdb=" C ASN J 157 " pdb=" N LYS J 158 " pdb=" CA LYS J 158 " ideal model delta harmonic sigma weight residual -180.00 -104.37 -75.63 0 5.00e+00 4.00e-02 2.29e+02 dihedral pdb=" CA LYS H 259 " pdb=" C LYS H 259 " pdb=" N PHE H 260 " pdb=" CA PHE H 260 " ideal model delta harmonic sigma weight residual -180.00 -114.95 -65.05 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA ASN m 32 " pdb=" C ASN m 32 " pdb=" N LYS m 33 " pdb=" CA LYS m 33 " ideal model delta harmonic sigma weight residual -180.00 -121.72 -58.28 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 81746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 26001 0.119 - 0.239: 1325 0.239 - 0.358: 152 0.358 - 0.477: 38 0.477 - 0.596: 9 Chirality restraints: 27525 Sorted by residual: chirality pdb=" C3' A 11900 " pdb=" C4' A 11900 " pdb=" O3' A 11900 " pdb=" C2' A 11900 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CB ILE p 133 " pdb=" CA ILE p 133 " pdb=" CG1 ILE p 133 " pdb=" CG2 ILE p 133 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" C3' G 3 77 " pdb=" C4' G 3 77 " pdb=" O3' G 3 77 " pdb=" C2' G 3 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 27522 not shown) Planarity restraints: 14178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG U 12 " -0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ARG U 12 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG U 12 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG U 13 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP c 46 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ASP c 46 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP c 46 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS c 47 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12046 " 0.052 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 U 12046 " -0.067 2.00e-02 2.50e+03 pdb=" C2 U 12046 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U 12046 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U 12046 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U 12046 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 12046 " 0.015 2.00e-02 2.50e+03 pdb=" C5 U 12046 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 12046 " -0.006 2.00e-02 2.50e+03 ... (remaining 14175 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 45362 2.86 - 3.54: 196455 3.54 - 4.22: 406668 4.22 - 4.90: 576020 Nonbonded interactions: 1224513 Sorted by model distance: nonbonded pdb=" CE2 TYR R 285 " pdb=" OP2 C B 72 " model vdw 1.501 3.340 nonbonded pdb=" OG1 THR A 345 " pdb=" NH1 ARG s 109 " model vdw 1.956 2.520 nonbonded pdb=" O2' G B 46 " pdb=" OP2 C B 48 " model vdw 2.023 2.440 nonbonded pdb=" NH2 ARG R 284 " pdb=" OP2 G B 1 " model vdw 2.037 2.520 nonbonded pdb=" O2' A B 58 " pdb=" OP2 U B 60 " model vdw 2.043 2.440 ... (remaining 1224508 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 21.020 Check model and map are aligned: 1.480 Set scattering table: 0.890 Process input model: 498.980 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 531.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.009 0.201 149194 Z= 0.534 Angle : 1.151 18.488 219385 Z= 0.611 Chirality : 0.063 0.596 27525 Planarity : 0.007 0.081 14178 Dihedral : 16.909 178.982 67413 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.24 % Favored : 91.40 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.08), residues: 7524 helix: -2.99 (0.07), residues: 2457 sheet: -1.92 (0.15), residues: 985 loop : -2.56 (0.08), residues: 4082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2352 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 2320 time to evaluate : 6.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 2341 average time/residue: 1.4202 time to fit residues: 5562.5121 Evaluate side-chains 1535 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1525 time to evaluate : 6.732 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 1.0335 time to fit residues: 28.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 940 optimal weight: 10.0000 chunk 844 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 569 optimal weight: 1.9990 chunk 451 optimal weight: 3.9990 chunk 873 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 649 optimal weight: 0.9990 chunk 1011 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 348 ASN A 352 GLN A 384 GLN A 457 HIS A 465 GLN A 470 GLN A 535 ASN A 562 ASN A 580 GLN R 29 ASN ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 GLN X 11 ASN X 162 HIS i 52 GLN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN j 16 GLN j 59 ASN K 38 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN 7 77 ASN 7 156 GLN l 79 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN M 109 HIS ** M 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 10 GLN m 40 GLN N 25 HIS N 37 ASN N 66 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN o 90 ASN p 37 HIS p 57 GLN p 156 HIS Q 122 GLN 5 34 GLN 5 64 ASN 5 97 ASN S 73 GLN s 143 ASN s 174 ASN T 92 GLN U 89 ASN U 122 HIS U 142 GLN U 157 GLN W 49 ASN ** x 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 98 ASN Y 32 GLN a 110 HIS b 36 HIS ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS d 12 GLN E 132 ASN E 194 ASN E 209 HIS F 3 HIS G 114 ASN G 260 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 ASN G 328 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN I 167 ASN L 35 GLN L 197 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 149194 Z= 0.229 Angle : 0.703 13.663 219385 Z= 0.370 Chirality : 0.042 0.362 27525 Planarity : 0.005 0.065 14178 Dihedral : 17.102 179.375 52524 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.96 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.09), residues: 7524 helix: -1.24 (0.09), residues: 2474 sheet: -1.50 (0.16), residues: 940 loop : -2.12 (0.09), residues: 4110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1700 time to evaluate : 6.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 244 outliers final: 170 residues processed: 1818 average time/residue: 1.2726 time to fit residues: 3965.1571 Evaluate side-chains 1606 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1436 time to evaluate : 8.434 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 1 residues processed: 170 average time/residue: 1.0608 time to fit residues: 351.6344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 562 optimal weight: 0.6980 chunk 313 optimal weight: 5.9990 chunk 841 optimal weight: 7.9990 chunk 688 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 1013 optimal weight: 7.9990 chunk 1094 optimal weight: 10.0000 chunk 902 optimal weight: 50.0000 chunk 1005 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 813 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN R 220 ASN ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN ** i 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 225 GLN j 61 GLN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 156 GLN 7 162 GLN l 76 ASN M 62 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 GLN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 GLN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 28 ASN S 45 ASN S 58 ASN S 126 GLN s 143 ASN s 174 ASN T 75 HIS ** x 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS C 82 GLN C 102 GLN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 ASN D 25 GLN E 38 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN h 42 GLN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 149194 Z= 0.410 Angle : 0.789 12.325 219385 Z= 0.408 Chirality : 0.046 0.450 27525 Planarity : 0.006 0.087 14178 Dihedral : 17.115 179.957 52524 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.15 % Favored : 91.63 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.09), residues: 7524 helix: -0.70 (0.10), residues: 2461 sheet: -1.56 (0.15), residues: 992 loop : -2.03 (0.09), residues: 4071 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1498 time to evaluate : 6.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 118 residues processed: 1622 average time/residue: 1.2501 time to fit residues: 3501.2498 Evaluate side-chains 1502 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1384 time to evaluate : 8.272 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 1 residues processed: 118 average time/residue: 1.0196 time to fit residues: 238.1554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 1001 optimal weight: 20.0000 chunk 761 optimal weight: 8.9990 chunk 525 optimal weight: 40.0000 chunk 112 optimal weight: 0.0170 chunk 483 optimal weight: 6.9990 chunk 680 optimal weight: 6.9990 chunk 1017 optimal weight: 6.9990 chunk 1076 optimal weight: 6.9990 chunk 531 optimal weight: 4.9990 chunk 963 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN A 470 GLN A 602 ASN R 29 ASN ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 361 ASN R 481 GLN i 3 GLN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN j 16 GLN j 62 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN l 79 GLN M 62 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 GLN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN Q 42 ASN Q 55 HIS 5 34 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 174 ASN r 56 ASN ** x 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 82 GLN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 GLN c 120 ASN d 43 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN E 218 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN h 42 GLN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.112 149194 Z= 0.394 Angle : 0.763 13.124 219385 Z= 0.394 Chirality : 0.046 0.606 27525 Planarity : 0.006 0.084 14178 Dihedral : 16.998 179.803 52524 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.32 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.09), residues: 7524 helix: -0.39 (0.10), residues: 2453 sheet: -1.47 (0.16), residues: 971 loop : -2.00 (0.09), residues: 4100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1466 time to evaluate : 8.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 142 residues processed: 1567 average time/residue: 1.2600 time to fit residues: 3422.2074 Evaluate side-chains 1503 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1361 time to evaluate : 6.857 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 1 residues processed: 142 average time/residue: 1.0082 time to fit residues: 281.5811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 896 optimal weight: 7.9990 chunk 611 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 801 optimal weight: 10.0000 chunk 444 optimal weight: 9.9990 chunk 918 optimal weight: 7.9990 chunk 744 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 549 optimal weight: 10.0000 chunk 966 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 ASN i 3 GLN ** i 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN l 79 GLN M 95 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 GLN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 195 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 174 ASN U 89 ASN V 26 HIS b 127 ASN ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 ASN d 10 HIS d 43 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.108 149194 Z= 0.497 Angle : 0.850 14.897 219385 Z= 0.434 Chirality : 0.049 0.552 27525 Planarity : 0.006 0.100 14178 Dihedral : 17.166 179.326 52524 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.50 % Favored : 90.28 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.09), residues: 7524 helix: -0.35 (0.10), residues: 2442 sheet: -1.57 (0.15), residues: 970 loop : -2.07 (0.09), residues: 4112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1428 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 120 residues processed: 1526 average time/residue: 1.2773 time to fit residues: 3395.5370 Evaluate side-chains 1470 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1350 time to evaluate : 6.733 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 1 residues processed: 120 average time/residue: 1.0413 time to fit residues: 247.1889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 362 optimal weight: 1.9990 chunk 969 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 632 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 1077 optimal weight: 10.0000 chunk 894 optimal weight: 4.9990 chunk 499 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 565 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN 7 183 HIS l 79 GLN M 62 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN p 57 GLN Q 29 ASN ** s 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 149194 Z= 0.244 Angle : 0.674 13.629 219385 Z= 0.351 Chirality : 0.041 0.517 27525 Planarity : 0.005 0.063 14178 Dihedral : 16.751 179.319 52524 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.15 % 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: -1.77 (0.09), residues: 7524 helix: 0.06 (0.11), residues: 2437 sheet: -1.38 (0.16), residues: 984 loop : -1.94 (0.09), residues: 4103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1487 time to evaluate : 6.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 80 residues processed: 1539 average time/residue: 1.2608 time to fit residues: 3348.1721 Evaluate side-chains 1455 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1375 time to evaluate : 8.329 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 1 residues processed: 80 average time/residue: 1.0131 time to fit residues: 157.6169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 1039 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 614 optimal weight: 5.9990 chunk 787 optimal weight: 7.9990 chunk 609 optimal weight: 7.9990 chunk 907 optimal weight: 7.9990 chunk 601 optimal weight: 5.9990 chunk 1073 optimal weight: 6.9990 chunk 671 optimal weight: 4.9990 chunk 654 optimal weight: 0.6980 chunk 495 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 156 GLN ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN l 79 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 70 ASN Q 182 ASN 5 72 GLN ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN U 63 GLN b 127 ASN ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 ASN d 43 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN F 279 ASN f 87 ASN ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 39 GLN L 21 ASN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 149194 Z= 0.319 Angle : 0.717 17.020 219385 Z= 0.371 Chirality : 0.043 0.439 27525 Planarity : 0.005 0.075 14178 Dihedral : 16.752 179.980 52524 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.86 % Favored : 90.95 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.16 % 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: -1.73 (0.09), residues: 7524 helix: 0.08 (0.11), residues: 2454 sheet: -1.38 (0.16), residues: 975 loop : -1.91 (0.09), residues: 4095 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1411 time to evaluate : 6.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 72 residues processed: 1459 average time/residue: 1.2451 time to fit residues: 3158.0932 Evaluate side-chains 1426 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1354 time to evaluate : 6.818 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 2 residues processed: 72 average time/residue: 1.0110 time to fit residues: 146.4209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 664 optimal weight: 0.2980 chunk 428 optimal weight: 20.0000 chunk 641 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 682 optimal weight: 8.9990 chunk 731 optimal weight: 9.9990 chunk 530 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 843 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 GLN ** j 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 GLN p 70 ASN S 73 GLN ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** U 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 ASN d 43 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN f 87 ASN ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 149194 Z= 0.262 Angle : 0.673 16.765 219385 Z= 0.350 Chirality : 0.041 0.385 27525 Planarity : 0.005 0.071 14178 Dihedral : 16.609 179.976 52524 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.32 % Favored : 91.52 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.18 % 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: -1.58 (0.09), residues: 7524 helix: 0.23 (0.11), residues: 2444 sheet: -1.24 (0.16), residues: 973 loop : -1.85 (0.09), residues: 4107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1419 time to evaluate : 6.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 68 residues processed: 1454 average time/residue: 1.2591 time to fit residues: 3172.4943 Evaluate side-chains 1416 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1348 time to evaluate : 6.784 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 2 residues processed: 68 average time/residue: 1.0318 time to fit residues: 140.5041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 976 optimal weight: 50.0000 chunk 1028 optimal weight: 30.0000 chunk 938 optimal weight: 8.9990 chunk 1000 optimal weight: 20.0000 chunk 602 optimal weight: 7.9990 chunk 435 optimal weight: 50.0000 chunk 785 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 904 optimal weight: 50.0000 chunk 946 optimal weight: 10.0000 chunk 997 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 ASN R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN K 28 HIS ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.116 149194 Z= 0.605 Angle : 0.940 17.807 219385 Z= 0.473 Chirality : 0.053 0.480 27525 Planarity : 0.007 0.107 14178 Dihedral : 17.231 179.935 52524 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.55 % Favored : 89.22 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.09), residues: 7524 helix: -0.23 (0.10), residues: 2460 sheet: -1.50 (0.16), residues: 964 loop : -2.09 (0.09), residues: 4100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1360 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 80 residues processed: 1401 average time/residue: 1.2980 time to fit residues: 3147.8647 Evaluate side-chains 1405 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1325 time to evaluate : 6.782 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 2 residues processed: 80 average time/residue: 1.0091 time to fit residues: 163.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 657 optimal weight: 1.9990 chunk 1058 optimal weight: 5.9990 chunk 645 optimal weight: 0.7980 chunk 501 optimal weight: 3.9990 chunk 735 optimal weight: 9.9990 chunk 1109 optimal weight: 10.0000 chunk 1021 optimal weight: 50.0000 chunk 883 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 682 optimal weight: 0.4980 chunk 541 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN p 70 ASN S 73 GLN ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 149194 Z= 0.254 Angle : 0.690 16.979 219385 Z= 0.358 Chirality : 0.042 0.365 27525 Planarity : 0.005 0.071 14178 Dihedral : 16.666 179.976 52524 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.72 % Favored : 92.11 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.19 % 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: -1.69 (0.09), residues: 7524 helix: 0.09 (0.11), residues: 2471 sheet: -1.32 (0.16), residues: 973 loop : -1.89 (0.09), residues: 4080 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1464 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1427 time to evaluate : 6.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 1438 average time/residue: 1.2839 time to fit residues: 3195.6053 Evaluate side-chains 1406 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1383 time to evaluate : 6.823 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 1.0212 time to fit residues: 53.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 701 optimal weight: 0.7980 chunk 941 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 814 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 885 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 chunk 908 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 HIS ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** j 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 162 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 GLN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 GLN p 57 GLN p 70 ASN ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN s 208 ASN x 24 ASN ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115378 restraints weight = 241898.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117145 restraints weight = 107110.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117668 restraints weight = 75043.239| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 149194 Z= 0.269 Angle : 0.694 17.393 219385 Z= 0.359 Chirality : 0.041 0.355 27525 Planarity : 0.005 0.067 14178 Dihedral : 16.602 179.999 52524 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.89 % Favored : 90.94 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.19 % 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: -1.60 (0.09), residues: 7524 helix: 0.15 (0.11), residues: 2475 sheet: -1.26 (0.16), residues: 992 loop : -1.82 (0.09), residues: 4057 =============================================================================== Job complete usr+sys time: 44956.06 seconds wall clock time: 781 minutes 36.90 seconds (46896.90 seconds total)