Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 07:30:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/07_2023/6oig_20077.pdb" } resolution = 3.8 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= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 3521 5.49 5 S 106 5.16 5 C 67636 2.51 5 N 23836 2.21 5 O 34041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 368": "NH1" <-> "NH2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 291": "NH1" <-> "NH2" Residue "H ARG 368": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 142": "NH1" <-> "NH2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "M ARG 257": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 175": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 217": "NH1" <-> "NH2" Residue "Q ARG 301": "NH1" <-> "NH2" Residue "Q ARG 303": "NH1" <-> "NH2" Residue "R ARG 197": "NH1" <-> "NH2" Residue "R ARG 245": "NH1" <-> "NH2" Residue "R TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 298": "NH1" <-> "NH2" Residue "R ARG 308": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "T PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 161": "NH1" <-> "NH2" Residue "W ARG 216": "NH1" <-> "NH2" Residue "W ARG 225": "NH1" <-> "NH2" Residue "W ARG 250": "NH1" <-> "NH2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X ARG 252": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Z PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 83": "NH1" <-> "NH2" Residue "Z TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "f TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 378": "NH1" <-> "NH2" Residue "g ARG 9": "NH1" <-> "NH2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 849": "NH1" <-> "NH2" Residue "j PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 18": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "q ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 129140 Number of models: 1 Model: "" Number of chains: 48 Chain: "z" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1602 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1918 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain: "B" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3082 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2750 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "D" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2376 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "E" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1240 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1785 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1818 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1519 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "I" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1718 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "J" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1354 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "s" 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: "L" 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: "M" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1054 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "N" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1721 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1556 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "P" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1443 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1442 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "R" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1522 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain: "S" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1446 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "T" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1277 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "U" 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: "V" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1004 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 4 Chain: "X" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "Y" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1174 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "b" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "c" 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: "d" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 890 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "e" 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: "f" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 772 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 682 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "k" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 613 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 418 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "o" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 848 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1077 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "5" Number of atoms: 69359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3243, 69359 Classifications: {'RNA': 3243} Modifications used: {'rna2p_pur': 328, 'rna2p_pyr': 219, 'rna3p_pur': 1466, 'rna3p_pyr': 1230} Link IDs: {'rna2p': 547, 'rna3p': 2695} Unresolved chain links: 1 Chain breaks: 9 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3354 Classifications: {'RNA': 158} Modifications used: {'p5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "7" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2580 Classifications: {'RNA': 121} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "x" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "y" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 230 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'TRANS': 45} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'UNK:plan-1': 46} Unresolved non-hydrogen planarities: 46 Residues with excluded nonbonded symmetry interactions: 198 residue: pdb=" N VAL z 208 " occ=0.80 ... (5 atoms not shown) pdb=" CG2 VAL z 208 " occ=0.80 residue: pdb=" N LYS z 209 " occ=0.80 ... (7 atoms not shown) pdb=" NZ LYS z 209 " occ=0.80 residue: pdb=" N GLU z 210 " occ=0.80 ... (7 atoms not shown) pdb=" OE2 GLU z 210 " occ=0.80 residue: pdb=" N LEU z 212 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU z 212 " occ=0.80 residue: pdb=" N LYS z 213 " occ=0.80 ... (7 atoms not shown) pdb=" NZ LYS z 213 " occ=0.80 residue: pdb=" N TYR z 214 " occ=0.80 ... (10 atoms not shown) pdb=" OH TYR z 214 " occ=0.80 residue: pdb=" N SER z 215 " occ=0.80 ... (4 atoms not shown) pdb=" OG SER z 215 " occ=0.80 residue: pdb=" N ASN z 216 " occ=0.80 ... (6 atoms not shown) pdb=" ND2 ASN z 216 " occ=0.80 residue: pdb=" N GLU z 217 " occ=0.80 ... (7 atoms not shown) pdb=" OE2 GLU z 217 " occ=0.80 residue: pdb=" N THR z 218 " occ=0.80 ... (5 atoms not shown) pdb=" CG2 THR z 218 " occ=0.80 residue: pdb=" N LYS z 219 " occ=0.80 ... (7 atoms not shown) pdb=" NZ LYS z 219 " occ=0.80 residue: pdb=" N LYS z 220 " occ=0.80 ... (7 atoms not shown) pdb=" NZ LYS z 220 " occ=0.80 ... (remaining 186 not shown) Time building chain proxies: 43.00, per 1000 atoms: 0.33 Number of scatterers: 129140 At special positions: 0 Unit cell: (265.36, 296.36, 260.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 3521 15.00 O 34041 8.00 N 23836 7.00 C 67636 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 Atom "ATOM 85728 O5' A 51545 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79649 O5' G 51262 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54720 O4' A 5 65 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78980 O5' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79522 O4' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54495 O4' G 5 55 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78725 O4' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79137 O4' C 51238 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59110 O4' U 5 270 .*. O " rejected from bonding due to valence issues. Atom "ATOM A028L O4' G 52465 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79111 O5' G 51237 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GX O5' C 52479 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80102 O4' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02AF O5' A 52468 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59042 O4' G 5 267 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0JV3 O5' C 8 142 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79629 O4' G 51261 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59258 O4' G 5 277 .*. O " rejected from bonding due to valence issues. Atom "ATOM A026P O5' A 52462 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54764 O4' A 5 67 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60092 O4' U 5 316 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78807 O5' A 51223 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79545 O4' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM 56029 O4' U 5 126 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85818 O4' U 51549 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80099 O5' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79604 O5' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59042 O4' G 5 267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60109 O5' A 5 317 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01JT O5' A 52424 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79951 O5' U 51276 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85818 O4' U 51549 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01M6 O5' U 52428 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79629 O4' G 51261 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54998 O5' U 5 78 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02F6 O5' C 52476 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54742 O4' A 5 66 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59752 O4' G 5 300 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79545 O4' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79783 O4' G 51268 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60198 O5' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54764 O4' A 5 67 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78957 O5' G 51230 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80099 O5' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55774 O4' A 5 114 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54495 O4' G 5 55 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60089 O5' U 5 316 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GD O5' C 52478 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79951 O5' U 51276 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59752 O4' G 5 300 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79763 O4' U 51267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59255 O5' G 5 277 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79565 O4' U 51258 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59147 O5' G 5 272 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79760 O5' U 51267 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02EJ O5' G 52475 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59110 O4' U 5 270 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02FQ O5' G 52477 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01ND O5' A 52430 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78725 O4' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59729 O4' G 5 299 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55774 O4' A 5 114 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59107 O5' U 5 270 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79091 O4' G 51236 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02PR O5' A 52494 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78980 O5' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79545 O4' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02AF O5' A 52468 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54475 O4' C 5 54 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02NH O5' C 52490 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79604 O5' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60198 O5' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79157 O4' C 51239 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79542 O5' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79542 O5' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GX O5' C 52479 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02PR O5' A 52494 .*. O " rejected from bonding due to valence issues. Atom "ATOM A04FW O5' C 52600 .*. O " rejected from bonding due to valence issues. Atom "ATOM A04FF O4' U 52599 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79545 O4' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78762 O5' A 51221 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80102 O4' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79763 O4' U 51267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80053 O5' G 51281 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79522 O4' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02B4 O4' G 52469 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79649 O5' G 51262 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79522 O4' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79519 O5' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60153 O5' A 5 319 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79519 O5' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01ND O5' A 52430 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79332 O4' U 51247 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59127 O5' C 5 271 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A028L O4' G 52465 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80016 O4' C 51279 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59127 O5' C 5 271 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79545 O4' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79154 O5' C 51239 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78725 O4' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54783 O5' C 5 68 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54675 O4' A 5 63 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79502 O4' C 51255 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78745 O4' U 51220 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60198 O5' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GX O5' C 52479 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79760 O5' U 51267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79519 O5' G 51256 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79607 O4' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54742 O4' A 5 66 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79675 O4' A 51263 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79309 O4' G 51246 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60092 O4' U 5 316 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79157 O4' C 51239 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60072 O4' C 5 315 .*. O " rejected from bonding due to valence issues. Atom "ATOM A028L O4' G 52465 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79542 O5' C 51257 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02N0 O4' C 52489 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78807 O5' A 51223 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80102 O4' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54783 O5' C 5 68 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02BO O5' C 52470 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79005 O4' C 51232 .*. O " rejected from bonding due to valence issues. Atom "ATOM A029S O5' G 52467 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59798 O4' U 5 302 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54675 O4' A 5 63 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85728 O5' A 51545 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85835 O5' C 51550 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54720 O4' A 5 65 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59127 O5' C 5 271 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59039 O5' G 5 267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79649 O5' G 51262 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A026P O5' A 52462 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02PR O5' A 52494 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78787 O4' G 51222 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80076 O5' G 51282 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78762 O5' A 51221 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80099 O5' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79284 O5' A 51245 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02BO O5' C 52470 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GD O5' C 52478 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78762 O5' A 51221 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54452 O4' G 5 53 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02B1 O5' G 52469 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0266 O4' A 52461 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79306 O5' G 51246 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86592 O5' G 51586 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79763 O4' U 51267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02HH O5' A 52480 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02FQ O5' G 52477 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78980 O5' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59582 O4' U 5 292 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79045 O5' G 51234 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54697 O4' G 5 64 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59110 O4' U 5 270 .*. O " rejected from bonding due to valence issues. Atom "ATOM 74259 O5' G 51010 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02EJ O5' G 52475 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01Y8 O4' G 52448 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59238 O4' U 5 276 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60131 O5' A 5 318 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55691 O4' G 5 110 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55001 O4' U 5 78 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54720 O4' A 5 65 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59042 O4' G 5 267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80076 O5' G 51282 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79502 O4' C 51255 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79867 O5' C 51272 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60201 O4' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79604 O5' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54764 O4' A 5 67 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78957 O5' G 51230 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80079 O4' G 51282 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78784 O5' G 51222 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78762 O5' A 51221 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02B1 O5' G 52469 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79604 O5' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79502 O4' C 51255 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79607 O4' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54720 O4' A 5 65 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60175 O5' G 5 320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A029V O4' G 52467 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80076 O5' G 51282 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59749 O5' G 5 300 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79091 O4' G 51236 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79585 O4' A 51259 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60134 O4' A 5 318 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54697 O4' G 5 64 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78765 O4' A 51221 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54492 O5' G 5 55 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78725 O4' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60201 O4' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54783 O5' C 5 68 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60153 O5' A 5 319 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78980 O5' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78722 O5' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01KI O4' G 52425 .*. O " rejected from bonding due to valence issues. Atom "ATOM A029V O4' G 52467 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79652 O4' G 51262 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79629 O4' G 51261 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02F6 O5' C 52476 .*. O " rejected from bonding due to valence issues. Atom "ATOM 56409 O4' A 5 144 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54783 O5' C 5 68 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59752 O4' G 5 300 .*. O " rejected from bonding due to valence issues. Atom "ATOM 56534 O5' A 5 150 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59258 O4' G 5 277 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79604 O5' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79951 O5' U 51276 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0JV3 O5' C 8 142 .*. O " rejected from bonding due to valence issues. Atom "ATOM 56029 O4' U 5 126 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59255 O5' G 5 277 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78705 O4' U 51218 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79991 O5' A 51278 .*. O " rejected from bonding due to valence issues. Atom "ATOM 56029 O4' U 5 126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0JV6 O4' C 8 142 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02FT O4' G 52477 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02H0 O4' C 52479 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0JV3 O5' C 8 142 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79971 O5' C 51277 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02PR O5' A 52494 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80056 O4' G 51281 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55774 O4' A 5 114 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54764 O4' A 5 67 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54998 O5' U 5 78 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79002 O5' C 51232 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78810 O4' A 51223 .*. O " rejected from bonding due to valence issues. Atom "ATOM 71974 O5' U 5 903 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0201 O5' G 52451 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59042 O4' G 5 267 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79607 O4' A 51260 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02MX O5' C 52489 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02LR O5' U 52487 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79565 O4' U 51258 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59107 O5' U 5 270 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59130 O4' C 5 271 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02NH O5' C 52490 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79137 O4' C 51238 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02FQ O5' G 52477 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0IE0 O4' A 8 52 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79971 O5' C 51277 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02B4 O4' G 52469 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59562 O4' C 5 291 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78787 O4' G 51222 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85731 O4' A 51545 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80076 O5' G 51282 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59729 O4' G 5 299 .*. O " rejected from bonding due to valence issues. Atom "ATOM A01M6 O5' U 52428 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54495 O4' G 5 55 .*. O " rejected from bonding due to valence issues. Atom "ATOM A029S O5' G 52467 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60201 O4' C 5 321 .*. O " rejected from bonding due to valence issues. Atom "ATOM A027E O4' G 52463 .*. O " rejected from bonding due to valence issues. Atom "ATOM A029V O4' G 52467 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02N0 O4' C 52489 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60089 O5' U 5 316 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78983 O4' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02HH O5' A 52480 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59729 O4' G 5 299 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0266 O4' A 52461 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54717 O5' A 5 65 .*. O " rejected from bonding due to valence issues. Atom "ATOM 80099 O5' C 51283 .*. O " rejected from bonding due to valence issues. Atom "ATOM 55669 O4' A 5 109 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78807 O5' A 51223 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02PU O4' A 52494 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60092 O4' U 5 316 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78980 O5' A 51231 .*. O " rejected from bonding due to valence issues. Atom "ATOM 78722 O5' C 51219 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79005 O4' C 51232 .*. O " rejected from bonding due to valence issues. Atom "ATOM 59582 O4' U 5 292 .*. O " rejected from bonding due to valence issues. Atom "ATOM A02GX O5' C 52479 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0263 O5' A 52461 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85835 O5' C 51550 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54427 O5' A 5 52 .*. O " rejected from bonding due to valence issues. Atom "ATOM 60241 O4' A 5 323 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79114 O4' G 51237 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 71.80 Conformation dependent library (CDL) restraints added in 6.5 seconds 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12822 Finding SS restraints... Secondary structure from input PDB file: 238 helices and 67 sheets defined 33.6% alpha, 10.0% beta 1115 base pairs and 1700 stacking pairs defined. Time for finding SS restraints: 43.11 Creating SS restraints... Processing helix chain 'z' and resid 304 through 309 removed outlier: 3.849A pdb=" N ALA z 307 " --> pdb=" O ALA z 304 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU z 309 " --> pdb=" O ILE z 306 " (cutoff:3.500A) Processing helix chain 'z' and resid 310 through 314 removed outlier: 3.563A pdb=" N LYS z 313 " --> pdb=" O VAL z 310 " (cutoff:3.500A) Processing helix chain 'z' and resid 368 through 372 Processing helix chain 'z' and resid 379 through 384 Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.612A pdb=" N ASP A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 182 through 193 removed outlier: 4.973A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.813A pdb=" N MET A 204 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.536A pdb=" N GLU B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.857A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 209' Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 161 through 170 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.528A pdb=" N LEU C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 330 through 335 removed outlier: 4.313A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 280 through 286 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.867A pdb=" N LYS D 303 " --> pdb=" O HIS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 Proline residue: D 344 - end of helix Processing helix chain 'D' and resid 354 through 374 Processing helix chain 'D' and resid 420 through 428 Processing helix chain 'D' and resid 451 through 460 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 466 through 474 removed outlier: 3.519A pdb=" N ASP D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'D' and resid 492 through 510 Processing helix chain 'D' and resid 523 through 532 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'E' and resid 292 through 297 Processing helix chain 'E' and resid 355 through 374 removed outlier: 3.709A pdb=" N ALA E 368 " --> pdb=" O VAL E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 384 Processing helix chain 'E' and resid 394 through 398 Processing helix chain 'F' and resid 236 through 283 removed outlier: 3.740A pdb=" N LYS F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 316 Processing helix chain 'F' and resid 330 through 338 removed outlier: 4.485A pdb=" N LYS F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 Processing helix chain 'F' and resid 375 through 384 Processing helix chain 'F' and resid 390 through 400 Processing helix chain 'F' and resid 404 through 412 Processing helix chain 'F' and resid 445 through 454 removed outlier: 3.838A pdb=" N LEU F 449 " --> pdb=" O PHE F 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 233 removed outlier: 4.298A pdb=" N LYS G 227 " --> pdb=" O GLN G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 260 removed outlier: 4.055A pdb=" N LYS G 260 " --> pdb=" O LYS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 276 Processing helix chain 'G' and resid 276 through 281 removed outlier: 3.681A pdb=" N ALA G 281 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 309 Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 329 through 337 Processing helix chain 'G' and resid 346 through 355 removed outlier: 4.059A pdb=" N THR G 352 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 353 " --> pdb=" O ARG G 349 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL G 354 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 386 Processing helix chain 'G' and resid 389 through 394 removed outlier: 4.097A pdb=" N VAL G 393 " --> pdb=" O LYS G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 414 through 419 removed outlier: 3.723A pdb=" N ASP G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 284 removed outlier: 5.109A pdb=" N THR H 270 " --> pdb=" O ALA H 266 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER H 273 " --> pdb=" O ARG H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 356 Processing helix chain 'H' and resid 356 through 363 Processing helix chain 'H' and resid 364 through 366 No H-bonds generated for 'chain 'H' and resid 364 through 366' Processing helix chain 'I' and resid 248 through 265 Processing helix chain 'I' and resid 266 through 270 removed outlier: 4.021A pdb=" N ALA I 269 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 343 removed outlier: 3.601A pdb=" N VAL I 333 " --> pdb=" O ASN I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 371 removed outlier: 3.785A pdb=" N LEU I 367 " --> pdb=" O ARG I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 397 Processing helix chain 'J' and resid 118 through 133 Processing helix chain 'J' and resid 164 through 178 Processing helix chain 'J' and resid 200 through 204 removed outlier: 3.812A pdb=" N LEU J 203 " --> pdb=" O HIS J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 Processing helix chain 'J' and resid 246 through 257 removed outlier: 3.744A pdb=" N LYS J 257 " --> pdb=" O TRP J 253 " (cutoff:3.500A) Processing helix chain 's' and resid 165 through 170 removed outlier: 3.804A pdb=" N GLY s 170 " --> pdb=" O PRO s 167 " (cutoff:3.500A) Processing helix chain 's' and resid 183 through 188 Processing helix chain 's' and resid 243 through 247 removed outlier: 3.931A pdb=" N ILE s 247 " --> pdb=" O ASP s 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 45 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 92 Processing helix chain 'L' and resid 105 through 119 removed outlier: 3.605A pdb=" N PHE L 109 " --> pdb=" O ASN L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'L' and resid 140 through 145 removed outlier: 3.815A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 179 removed outlier: 3.722A pdb=" N ALA L 173 " --> pdb=" O THR L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 192 removed outlier: 3.952A pdb=" N GLU L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS L 185 " --> pdb=" O GLY L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 212 No H-bonds generated for 'chain 'M' and resid 210 through 212' Processing helix chain 'M' and resid 226 through 237 Processing helix chain 'M' and resid 240 through 245 Processing helix chain 'M' and resid 246 through 259 Processing helix chain 'M' and resid 262 through 281 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.585A pdb=" N ARG N 20 " --> pdb=" O SER N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 84 through 88 removed outlier: 4.163A pdb=" N GLY N 88 " --> pdb=" O THR N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 107 removed outlier: 3.801A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 159 through 163 removed outlier: 3.581A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 173 removed outlier: 3.922A pdb=" N SER N 171 " --> pdb=" O THR N 167 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 195 removed outlier: 3.853A pdb=" N LYS N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 27 removed outlier: 4.313A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU O 27 " --> pdb=" O VAL O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 46 through 59 removed outlier: 4.558A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG O 59 " --> pdb=" O HIS O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.677A pdb=" N ALA O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 149 through 182 removed outlier: 4.401A pdb=" N VAL O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 186 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 35 Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.524A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 100 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 171 through 183 removed outlier: 3.850A pdb=" N ALA P 183 " --> pdb=" O GLN P 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 148 through 164 Processing helix chain 'Q' and resid 167 through 177 removed outlier: 3.727A pdb=" N LYS Q 171 " --> pdb=" O ALA Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 195 Processing helix chain 'Q' and resid 232 through 240 Processing helix chain 'Q' and resid 249 through 256 Processing helix chain 'R' and resid 140 through 151 Processing helix chain 'R' and resid 163 through 168 Processing helix chain 'R' and resid 172 through 182 Processing helix chain 'R' and resid 195 through 207 Processing helix chain 'R' and resid 219 through 224 Processing helix chain 'R' and resid 226 through 247 Processing helix chain 'R' and resid 251 through 265 removed outlier: 4.607A pdb=" N LYS R 260 " --> pdb=" O HIS R 256 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 265 " --> pdb=" O GLU R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 4.243A pdb=" N LEU R 290 " --> pdb=" O ARG R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 313 Processing helix chain 'R' and resid 314 through 316 No H-bonds generated for 'chain 'R' and resid 314 through 316' Processing helix chain 'S' and resid 33 through 49 removed outlier: 4.040A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.866A pdb=" N ALA S 102 " --> pdb=" O SER S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 131 through 135 removed outlier: 3.921A pdb=" N VAL S 135 " --> pdb=" O THR S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'T' and resid 26 through 31 removed outlier: 3.976A pdb=" N TYR T 30 " --> pdb=" O HIS T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.988A pdb=" N GLN T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 107 Processing helix chain 'T' and resid 108 through 113 Processing helix chain 'T' and resid 113 through 122 Processing helix chain 'U' and resid 98 through 103 removed outlier: 4.085A pdb=" N THR U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 118 removed outlier: 3.779A pdb=" N ASP U 118 " --> pdb=" O LYS U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 151 through 166 removed outlier: 3.734A pdb=" N LYS U 161 " --> pdb=" O TYR U 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 199 Processing helix chain 'V' and resid 248 through 255 Processing helix chain 'V' and resid 255 through 262 Processing helix chain 'W' and resid 178 through 187 Processing helix chain 'W' and resid 190 through 194 removed outlier: 3.626A pdb=" N ILE W 194 " --> pdb=" O PRO W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 205 Processing helix chain 'W' and resid 232 through 237 Processing helix chain 'W' and resid 242 through 253 Processing helix chain 'W' and resid 255 through 263 removed outlier: 3.626A pdb=" N LYS W 260 " --> pdb=" O ALA W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 278 Processing helix chain 'X' and resid 172 through 176 Processing helix chain 'X' and resid 183 through 193 Processing helix chain 'X' and resid 205 through 218 removed outlier: 3.946A pdb=" N LYS X 214 " --> pdb=" O LYS X 210 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU X 215 " --> pdb=" O LYS X 211 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU X 216 " --> pdb=" O ALA X 212 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR X 217 " --> pdb=" O VAL X 213 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 251 removed outlier: 3.598A pdb=" N ASN X 251 " --> pdb=" O LEU X 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 16 Processing helix chain 'Y' and resid 17 through 21 removed outlier: 4.247A pdb=" N PHE Y 20 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR Y 21 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 17 through 21' Processing helix chain 'Y' and resid 26 through 31 removed outlier: 3.952A pdb=" N LEU Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 26 through 31' Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 104 removed outlier: 3.662A pdb=" N LYS Y 103 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 122 removed outlier: 3.523A pdb=" N LYS Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 77 No H-bonds generated for 'chain 'Z' and resid 75 through 77' Processing helix chain 'Z' and resid 88 through 93 removed outlier: 4.371A pdb=" N SER Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 122 removed outlier: 3.855A pdb=" N ARG Z 106 " --> pdb=" O GLN Z 102 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL Z 112 " --> pdb=" O GLU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 125 No H-bonds generated for 'chain 'Z' and resid 123 through 125' Processing helix chain 'Z' and resid 126 through 131 Processing helix chain 'a' and resid 83 through 93 removed outlier: 3.761A pdb=" N THR a 87 " --> pdb=" O SER a 84 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS a 88 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR a 89 " --> pdb=" O PHE a 86 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG a 93 " --> pdb=" O ARG a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 128 removed outlier: 3.836A pdb=" N LYS a 128 " --> pdb=" O ILE a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 150 removed outlier: 3.674A pdb=" N TRP a 150 " --> pdb=" O ALA a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 174 Processing helix chain 'a' and resid 212 through 223 Processing helix chain 'b' and resid 78 through 83 Processing helix chain 'b' and resid 102 through 113 removed outlier: 4.552A pdb=" N HIS b 111 " --> pdb=" O ARG b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 122 Processing helix chain 'c' and resid 10 through 21 removed outlier: 3.561A pdb=" N ILE c 18 " --> pdb=" O LEU c 14 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 36 Processing helix chain 'c' and resid 49 through 63 Processing helix chain 'c' and resid 74 through 79 Processing helix chain 'd' and resid 85 through 103 removed outlier: 3.531A pdb=" N MET d 102 " --> pdb=" O ALA d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 118 Processing helix chain 'e' and resid 172 through 176 Processing helix chain 'e' and resid 230 through 235 removed outlier: 4.264A pdb=" N THR e 235 " --> pdb=" O LYS e 231 " (cutoff:3.500A) Processing helix chain 'e' and resid 252 through 267 removed outlier: 3.745A pdb=" N VAL e 258 " --> pdb=" O LYS e 254 " (cutoff:3.500A) Processing helix chain 'f' and resid 355 through 357 No H-bonds generated for 'chain 'f' and resid 355 through 357' Processing helix chain 'f' and resid 358 through 363 removed outlier: 4.501A pdb=" N TYR f 362 " --> pdb=" O ASP f 358 " (cutoff:3.500A) Processing helix chain 'f' and resid 393 through 397 removed outlier: 4.353A pdb=" N SER f 396 " --> pdb=" O HIS f 393 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY f 397 " --> pdb=" O GLY f 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 393 through 397' Processing helix chain 'g' and resid 58 through 62 removed outlier: 3.673A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.716A pdb=" N LYS g 70 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 110 removed outlier: 3.630A pdb=" N LYS g 103 " --> pdb=" O LYS g 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 12 Processing helix chain 'h' and resid 13 through 36 Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.727A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 99 removed outlier: 3.905A pdb=" N GLN h 99 " --> pdb=" O GLU h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 removed outlier: 3.857A pdb=" N PHE h 111 " --> pdb=" O LYS h 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 66 through 78 removed outlier: 3.556A pdb=" N LEU i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 97 Processing helix chain 'j' and resid 790 through 795 Processing helix chain 'j' and resid 837 through 842 Processing helix chain 'j' and resid 855 through 863 Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 58 through 67 Processing helix chain 'l' and resid 6 through 18 removed outlier: 3.841A pdb=" N LYS l 18 " --> pdb=" O ALA l 14 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.701A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 90 Processing helix chain 'm' and resid 112 through 116 removed outlier: 3.885A pdb=" N CYS m 115 " --> pdb=" O LYS m 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 48 removed outlier: 4.143A pdb=" N SER o 48 " --> pdb=" O ASP o 44 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 14 removed outlier: 3.695A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 34 removed outlier: 3.533A pdb=" N ARG p 23 " --> pdb=" O GLY p 19 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS p 28 " --> pdb=" O ARG p 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 86 Processing helix chain 'p' and resid 86 through 91 Processing helix chain 'q' and resid 4 through 12 Processing helix chain 'q' and resid 13 through 18 removed outlier: 4.282A pdb=" N TYR q 18 " --> pdb=" O LYS q 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 36 through 41 Processing helix chain 'q' and resid 59 through 65 Processing helix chain 'q' and resid 70 through 77 removed outlier: 3.554A pdb=" N GLU q 74 " --> pdb=" O PRO q 71 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS q 75 " --> pdb=" O ASP q 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU q 76 " --> pdb=" O PHE q 73 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 101 removed outlier: 4.109A pdb=" N VAL q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 210 through 213 removed outlier: 3.609A pdb=" N UNK q 213 " --> pdb=" O UNK q 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 210 through 213' Processing helix chain 'q' and resid 214 through 219 Processing helix chain 'x' and resid 21 through 29 Processing helix chain 'y' and resid 21 through 29 Processing sheet with id=AA1, first strand: chain 'z' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'z' and resid 263 through 264 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 77 removed outlier: 4.013A pdb=" N ARG A 70 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ALA A 56 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS A 50 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG A 64 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ARG A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 4.416A pdb=" N LEU A 102 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 164 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'B' and resid 356 through 358 removed outlier: 6.183A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 325 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 322 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 106 removed outlier: 4.936A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 85 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 162 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 179 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 106 removed outlier: 4.936A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 20 removed outlier: 5.103A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.415A pdb=" N GLU C 63 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 76 " --> pdb=" O GLU C 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 333 through 338 removed outlier: 3.904A pdb=" N VAL D 333 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 326 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D 324 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA D 337 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS D 322 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 319 " --> pdb=" O THR D 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 443 through 444 Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 266 removed outlier: 5.839A pdb=" N VAL E 263 " --> pdb=" O THR E 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 277 through 282 removed outlier: 4.897A pdb=" N TYR E 278 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER E 290 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 285 through 286 Processing sheet with id=AB8, first strand: chain 'F' and resid 363 through 364 removed outlier: 3.542A pdb=" N VAL F 371 " --> pdb=" O GLY F 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 234 through 235 Processing sheet with id=AC1, first strand: chain 'G' and resid 315 through 318 removed outlier: 6.216A pdb=" N VAL G 315 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE G 317 " --> pdb=" O VAL G 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'H' and resid 203 through 206 removed outlier: 6.105A pdb=" N ILE H 204 " --> pdb=" O ASN H 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 209 through 210 Processing sheet with id=AC4, first strand: chain 'H' and resid 218 through 220 removed outlier: 3.931A pdb=" N ILE M 155 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 225 through 228 removed outlier: 3.943A pdb=" N VAL H 225 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 236 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 335 through 336 removed outlier: 3.696A pdb=" N ILE H 344 " --> pdb=" O MET H 290 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG H 291 " --> pdb=" O VAL H 381 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL H 381 " --> pdb=" O ARG H 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 300 through 302 Processing sheet with id=AC8, first strand: chain 'I' and resid 323 through 325 Processing sheet with id=AC9, first strand: chain 'I' and resid 243 through 245 removed outlier: 6.248A pdb=" N LEU I 282 " --> pdb=" O HIS I 308 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU I 310 " --> pdb=" O HIS I 280 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS I 280 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.009A pdb=" N LEU I 361 " --> pdb=" O TRP I 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 376 through 377 Processing sheet with id=AD3, first strand: chain 'J' and resid 161 through 163 removed outlier: 4.690A pdb=" N ILE J 105 " --> pdb=" O ASN J 223 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN J 223 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 138 through 139 Processing sheet with id=AD5, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD6, first strand: chain 'M' and resid 170 through 171 removed outlier: 5.286A pdb=" N ILE M 184 " --> pdb=" O ASP M 196 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP M 196 " --> pdb=" O ILE M 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 193 " --> pdb=" O ILE M 207 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY M 197 " --> pdb=" O PRO M 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 59 through 67 removed outlier: 3.531A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 59 through 67 removed outlier: 3.531A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 6 through 10 removed outlier: 5.478A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE O 33 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'P' and resid 14 through 16 removed outlier: 3.934A pdb=" N ALA P 15 " --> pdb=" O VAL P 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL P 150 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE P 146 " --> pdb=" O SER P 20 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER P 20 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 14 through 16 removed outlier: 3.934A pdb=" N ALA P 15 " --> pdb=" O VAL P 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL P 150 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS P 116 " --> pdb=" O VAL P 149 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AE4, first strand: chain 'S' and resid 25 through 27 Processing sheet with id=AE5, first strand: chain 'S' and resid 88 through 93 removed outlier: 5.868A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 83 through 92 removed outlier: 5.538A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 135 through 136 removed outlier: 8.269A pdb=" N TYR U 182 " --> pdb=" O THR U 93 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THR U 95 " --> pdb=" O TYR U 182 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 146 through 147 removed outlier: 4.177A pdb=" N LEU V 146 " --> pdb=" O ALA V 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 151 through 154 removed outlier: 4.805A pdb=" N ILE V 165 " --> pdb=" O THR V 190 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR V 190 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL V 187 " --> pdb=" O ALA V 205 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA V 205 " --> pdb=" O VAL V 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL V 191 " --> pdb=" O LYS V 201 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS V 201 " --> pdb=" O VAL V 191 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLY V 229 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASN V 153 " --> pdb=" O GLY V 229 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE V 231 " --> pdb=" O ASN V 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 214 through 216 Processing sheet with id=AF2, first strand: chain 'W' and resid 166 through 167 Processing sheet with id=AF3, first strand: chain 'X' and resid 177 through 179 Processing sheet with id=AF4, first strand: chain 'X' and resid 195 through 196 removed outlier: 7.263A pdb=" N LYS X 235 " --> pdb=" O THR X 226 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR X 226 " --> pdb=" O LYS X 235 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR X 237 " --> pdb=" O VAL X 224 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL X 224 " --> pdb=" O TYR X 237 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG X 239 " --> pdb=" O LEU X 222 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 70 through 74 removed outlier: 6.750A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 69 through 72 removed outlier: 6.287A pdb=" N LEU Z 41 " --> pdb=" O VAL Z 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE Z 45 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS Z 21 " --> pdb=" O ILE Z 45 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS Z 8 " --> pdb=" O ILE Z 24 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL Z 9 " --> pdb=" O THR Z 82 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 182 through 184 removed outlier: 5.660A pdb=" N ILE a 183 " --> pdb=" O LYS a 207 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 22 through 24 removed outlier: 6.755A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 107 through 109 removed outlier: 6.450A pdb=" N ARG d 108 " --> pdb=" O VAL d 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER d 134 " --> pdb=" O TYR d 150 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU d 152 " --> pdb=" O ARG d 132 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG d 132 " --> pdb=" O GLU d 152 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR d 67 " --> pdb=" O VAL d 167 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 226 through 227 Processing sheet with id=AG2, first strand: chain 'f' and resid 329 through 334 removed outlier: 6.450A pdb=" N LEU f 347 " --> pdb=" O LEU f 332 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 382 through 387 Processing sheet with id=AG4, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG5, first strand: chain 'j' and resid 802 through 803 removed outlier: 3.552A pdb=" N THR j 819 " --> pdb=" O HIS j 814 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 22 through 25 removed outlier: 6.308A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'k' and resid 30 through 31 Processing sheet with id=AG8, first strand: chain 'm' and resid 101 through 103 removed outlier: 3.667A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'o' and resid 10 through 11 Processing sheet with id=AH1, first strand: chain 'o' and resid 23 through 27 Processing sheet with id=AH2, first strand: chain 'p' and resid 37 through 38 removed outlier: 5.800A pdb=" N ARG p 49 " --> pdb=" O THR p 56 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR p 56 " --> pdb=" O ARG p 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA p 51 " --> pdb=" O ILE p 54 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 51 through 53 Processing sheet with id=AH4, first strand: chain 'x' and resid 14 through 15 1555 hydrogen bonds defined for protein. 4323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2715 hydrogen bonds 4224 hydrogen bond angles 0 basepair planarities 1115 basepair parallelities 1700 stacking parallelities Total time for adding SS restraints: 195.46 Time building geometry restraints manager: 76.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 1.03: 1 1.03 - 1.45: 73398 1.45 - 1.87: 65612 1.87 - 2.28: 1 2.28 - 2.70: 2 Bond restraints: 139014 Sorted by residual: bond pdb=" O3' G 52246 " pdb=" P G 52247 " ideal model delta sigma weight residual 1.607 2.702 -1.095 1.50e-02 4.44e+03 5.33e+03 bond pdb=" CA VAL R 312 " pdb=" C VAL R 312 " ideal model delta sigma weight residual 1.520 2.346 -0.826 1.20e-02 6.94e+03 4.74e+03 bond pdb=" O3' C 52263 " pdb=" P U 52264 " ideal model delta sigma weight residual 1.607 0.611 0.996 1.50e-02 4.44e+03 4.41e+03 bond pdb=" O3' A 52279 " pdb=" P A 52280 " ideal model delta sigma weight residual 1.607 1.963 -0.356 1.50e-02 4.44e+03 5.62e+02 bond pdb=" CA CYS o 12 " pdb=" CB CYS o 12 " ideal model delta sigma weight residual 1.524 1.359 0.165 1.33e-02 5.65e+03 1.54e+02 ... (remaining 139009 not shown) Histogram of bond angle deviations from ideal: 45.23 - 68.75: 2 68.75 - 92.27: 6 92.27 - 115.79: 116849 115.79 - 139.30: 88005 139.30 - 162.82: 6 Bond angle restraints: 204868 Sorted by residual: angle pdb=" O3' A 52279 " pdb=" P A 52280 " pdb=" O5' A 52280 " ideal model delta sigma weight residual 104.00 45.23 58.77 1.50e+00 4.44e-01 1.54e+03 angle pdb=" C3' A 52279 " pdb=" O3' A 52279 " pdb=" P A 52280 " ideal model delta sigma weight residual 120.20 162.82 -42.62 1.50e+00 4.44e-01 8.07e+02 angle pdb=" C VAL R 312 " pdb=" CA VAL R 312 " pdb=" CB VAL R 312 " ideal model delta sigma weight residual 110.62 138.62 -28.00 1.08e+00 8.57e-01 6.72e+02 angle pdb=" C3' C 52263 " pdb=" O3' C 52263 " pdb=" P U 52264 " ideal model delta sigma weight residual 120.20 158.69 -38.49 1.50e+00 4.44e-01 6.58e+02 angle pdb=" O3' C 52263 " pdb=" P U 52264 " pdb=" OP2 U 52264 " ideal model delta sigma weight residual 108.00 56.54 51.46 3.00e+00 1.11e-01 2.94e+02 ... (remaining 204863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 70683 35.97 - 71.93: 4801 71.93 - 107.90: 467 107.90 - 143.86: 29 143.86 - 179.83: 39 Dihedral angle restraints: 76019 sinusoidal: 56162 harmonic: 19857 Sorted by residual: dihedral pdb=" C VAL R 312 " pdb=" N VAL R 312 " pdb=" CA VAL R 312 " pdb=" CB VAL R 312 " ideal model delta harmonic sigma weight residual -122.00 -149.40 27.40 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" CA LYS F 368 " pdb=" C LYS F 368 " pdb=" N GLN F 369 " pdb=" CA GLN F 369 " ideal model delta harmonic sigma weight residual 180.00 127.91 52.09 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA SER s 257 " pdb=" C SER s 257 " pdb=" N PHE s 258 " pdb=" CA PHE s 258 " ideal model delta harmonic sigma weight residual -180.00 -130.61 -49.39 0 5.00e+00 4.00e-02 9.76e+01 ... (remaining 76016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 25734 0.401 - 0.802: 8 0.802 - 1.203: 0 1.203 - 1.604: 0 1.604 - 2.005: 2 Chirality restraints: 25744 Sorted by residual: chirality pdb=" P A 53305 " pdb=" OP1 A 53305 " pdb=" OP2 A 53305 " pdb=" O5' A 53305 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" CB VAL R 312 " pdb=" CA VAL R 312 " pdb=" CG1 VAL R 312 " pdb=" CG2 VAL R 312 " both_signs ideal model delta sigma weight residual False -2.63 -0.93 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1' A 5 11 " pdb=" O4' A 5 11 " pdb=" C2' A 5 11 " pdb=" N9 A 5 11 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 25741 not shown) Planarity restraints: 12919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 52248 " 0.081 2.00e-02 2.50e+03 3.96e-02 3.52e+01 pdb=" N1 C 52248 " -0.012 2.00e-02 2.50e+03 pdb=" C2 C 52248 " -0.016 2.00e-02 2.50e+03 pdb=" O2 C 52248 " -0.034 2.00e-02 2.50e+03 pdb=" N3 C 52248 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C 52248 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C 52248 " 0.053 2.00e-02 2.50e+03 pdb=" C5 C 52248 " -0.030 2.00e-02 2.50e+03 pdb=" C6 C 52248 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 52258 " 0.062 2.00e-02 2.50e+03 3.62e-02 2.94e+01 pdb=" N1 U 52258 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U 52258 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U 52258 " -0.020 2.00e-02 2.50e+03 pdb=" N3 U 52258 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 52258 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U 52258 " 0.069 2.00e-02 2.50e+03 pdb=" C5 U 52258 " -0.036 2.00e-02 2.50e+03 pdb=" C6 U 52258 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 52278 " 0.070 2.00e-02 2.50e+03 3.48e-02 2.72e+01 pdb=" N1 C 52278 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C 52278 " -0.011 2.00e-02 2.50e+03 pdb=" O2 C 52278 " -0.035 2.00e-02 2.50e+03 pdb=" N3 C 52278 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 52278 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 52278 " 0.046 2.00e-02 2.50e+03 pdb=" C5 C 52278 " -0.031 2.00e-02 2.50e+03 pdb=" C6 C 52278 " -0.039 2.00e-02 2.50e+03 ... (remaining 12916 not shown) Histogram of nonbonded interaction distances: 0.09 - 1.05: 719 1.05 - 2.01: 4450 2.01 - 2.97: 79496 2.97 - 3.94: 489059 3.94 - 4.90: 784555 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1358279 Sorted by model distance: nonbonded pdb=" O ILE z 260 " pdb=" OP2 G 52481 " model vdw 0.087 3.040 nonbonded pdb=" CA ASN q 83 " pdb=" C8 G 51282 " model vdw 0.104 3.690 nonbonded pdb=" CB PHE N 21 " pdb=" C1' C 5 315 " model vdw 0.120 3.870 nonbonded pdb=" NH2 ARG N 188 " pdb=" O5' A 51545 " model vdw 0.126 2.520 nonbonded pdb=" O LEU z 411 " pdb=" N9 G 52448 " model vdw 0.143 3.120 ... (remaining 1358274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and resid 2 through 47) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 19.840 Check model and map are aligned: 1.390 Set scattering table: 0.830 Process input model: 447.380 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 478.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 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 : 0.011 1.095 139014 Z= 0.639 Angle : 1.450 58.771 204868 Z= 0.736 Chirality : 0.071 2.005 25744 Planarity : 0.009 0.107 12919 Dihedral : 19.618 179.827 63197 Min Nonbonded Distance : 0.087 Molprobity Statistics. All-atom Clashscore : 53.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.86 % Favored : 83.89 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 1.26 % 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: -5.09 (0.08), residues: 6650 helix: -3.70 (0.07), residues: 1942 sheet: -3.32 (0.17), residues: 689 loop : -3.36 (0.08), residues: 4019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1955 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1889 time to evaluate : 6.389 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL z 396 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 66 outliers final: 15 residues processed: 1939 average time/residue: 1.2953 time to fit residues: 4189.0195 Evaluate side-chains 958 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 943 time to evaluate : 5.717 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 1.1132 time to fit residues: 34.8824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 858 optimal weight: 9.9990 chunk 770 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 519 optimal weight: 9.9990 chunk 411 optimal weight: 10.0000 chunk 797 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 593 optimal weight: 8.9990 chunk 923 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 335 HIS A 83 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 269 GLN C 45 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN F 247 ASN F 314 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN G 385 ASN G 407 GLN H 208 GLN ** H 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 HIS H 316 ASN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN L 102 GLN M 254 GLN ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 GLN Q 277 HIS R 162 ASN R 203 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 227 ASN ** W 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 279 GLN X 194 ASN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 HIS ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 177 HIS e 182 ASN ** f 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 360 GLN ** f 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN i 92 ASN ** j 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 43 ASN ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN p 34 HIS ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.870 139014 Z= 0.825 Angle : 1.587 80.533 204868 Z= 0.762 Chirality : 0.071 1.863 25744 Planarity : 0.011 0.311 12919 Dihedral : 20.993 179.913 49876 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 56.29 Ramachandran Plot: Outliers : 0.77 % Allowed : 13.11 % Favored : 86.12 % Rotamer Outliers : 5.98 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.95 % Twisted General : 1.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.09), residues: 6650 helix: -2.56 (0.09), residues: 1991 sheet: -3.00 (0.18), residues: 674 loop : -3.18 (0.09), residues: 3985 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1115 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL z 396 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 330 outliers final: 186 residues processed: 1332 average time/residue: 1.2215 time to fit residues: 2812.6071 Evaluate side-chains 983 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 797 time to evaluate : 6.321 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 2 residues processed: 186 average time/residue: 1.0697 time to fit residues: 372.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 768 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 925 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 chunk 823 optimal weight: 20.0000 chunk 917 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 742 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 392 ASN z 394 GLN A 194 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN H 250 ASN ** H 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN J 181 GLN L 17 HIS L 19 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** N 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 50 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 HIS ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 406 ASN ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 855 HIS ** j 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 67 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.860 139014 Z= 0.772 Angle : 1.317 60.160 204868 Z= 0.653 Chirality : 0.063 1.894 25744 Planarity : 0.010 0.343 12919 Dihedral : 20.297 179.842 49876 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 49.03 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.00 % Favored : 85.47 % Rotamer Outliers : 5.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % Twisted General : 1.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.09), residues: 6650 helix: -1.96 (0.10), residues: 2038 sheet: -2.80 (0.16), residues: 771 loop : -3.18 (0.09), residues: 3841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 989 time to evaluate : 6.469 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL z 396 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 316 outliers final: 150 residues processed: 1218 average time/residue: 1.1786 time to fit residues: 2488.2761 Evaluate side-chains 905 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 755 time to evaluate : 6.468 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 3 residues processed: 150 average time/residue: 1.0686 time to fit residues: 298.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 914 optimal weight: 20.0000 chunk 695 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 441 optimal weight: 50.0000 chunk 621 optimal weight: 6.9990 chunk 928 optimal weight: 10.0000 chunk 983 optimal weight: 10.0000 chunk 485 optimal weight: 5.9990 chunk 880 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 289 ASN A 194 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 GLN E 391 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN G 287 GLN H 208 GLN ** H 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 357 ASN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS P 54 HIS ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 GLN ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 GLN ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 88 GLN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 261 ASN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 ASN ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 HIS ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 32 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.8378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.867 139014 Z= 0.706 Angle : 1.162 50.103 204868 Z= 0.576 Chirality : 0.059 2.814 25744 Planarity : 0.008 0.119 12919 Dihedral : 19.708 179.678 49876 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 43.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.53 % Favored : 86.09 % Rotamer Outliers : 5.07 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.34 % Twisted General : 0.90 % 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: -3.64 (0.09), residues: 6650 helix: -1.42 (0.10), residues: 2038 sheet: -2.48 (0.17), residues: 752 loop : -3.11 (0.09), residues: 3860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 887 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL z 396 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 280 outliers final: 150 residues processed: 1081 average time/residue: 1.1232 time to fit residues: 2107.2125 Evaluate side-chains 879 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 729 time to evaluate : 6.528 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 150 outliers final: 2 residues processed: 150 average time/residue: 1.0056 time to fit residues: 280.8304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 818 optimal weight: 20.0000 chunk 558 optimal weight: 0.1980 chunk 14 optimal weight: 30.0000 chunk 731 optimal weight: 20.0000 chunk 405 optimal weight: 4.9990 chunk 838 optimal weight: 10.0000 chunk 679 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 882 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 383 ASN A 194 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN D 534 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 GLN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 HIS ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 360 ASN ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 HIS S 157 GLN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 61 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 GLN ** q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.9036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.885 139014 Z= 0.650 Angle : 1.047 51.783 204868 Z= 0.522 Chirality : 0.051 1.994 25744 Planarity : 0.007 0.106 12919 Dihedral : 19.146 179.489 49876 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 35.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.75 % Favored : 86.95 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.74 % 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: -3.27 (0.09), residues: 6650 helix: -0.99 (0.11), residues: 2037 sheet: -2.33 (0.17), residues: 760 loop : -2.94 (0.09), residues: 3853 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 862 time to evaluate : 6.442 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 outliers start: 183 outliers final: 77 residues processed: 989 average time/residue: 1.1592 time to fit residues: 2003.1417 Evaluate side-chains 803 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 726 time to evaluate : 6.424 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 77 outliers final: 2 residues processed: 77 average time/residue: 1.0425 time to fit residues: 151.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 577 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 983 optimal weight: 10.0000 chunk 816 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 394 GLN A 97 ASN A 194 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 356 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 360 ASN I 394 ASN J 153 ASN ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS U 128 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 HIS ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 59 HIS ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.9935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.876 139014 Z= 0.661 Angle : 1.048 52.357 204868 Z= 0.526 Chirality : 0.052 1.941 25744 Planarity : 0.007 0.139 12919 Dihedral : 19.126 179.996 49876 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 39.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.77 % Favored : 86.00 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.73 % 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: -3.20 (0.09), residues: 6650 helix: -0.94 (0.11), residues: 2039 sheet: -2.08 (0.18), residues: 717 loop : -2.94 (0.09), residues: 3894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 787 time to evaluate : 6.386 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 outliers start: 214 outliers final: 122 residues processed: 933 average time/residue: 1.1015 time to fit residues: 1807.2843 Evaluate side-chains 816 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 694 time to evaluate : 6.371 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 122 outliers final: 2 residues processed: 122 average time/residue: 1.0428 time to fit residues: 234.4165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 948 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 560 optimal weight: 0.5980 chunk 718 optimal weight: 10.0000 chunk 556 optimal weight: 7.9990 chunk 828 optimal weight: 20.0000 chunk 549 optimal weight: 2.9990 chunk 980 optimal weight: 20.0000 chunk 613 optimal weight: 30.0000 chunk 597 optimal weight: 7.9990 chunk 452 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 798 HIS k 67 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 1.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.886 139014 Z= 0.638 Angle : 0.986 45.016 204868 Z= 0.499 Chirality : 0.050 1.947 25744 Planarity : 0.007 0.079 12919 Dihedral : 18.815 179.772 49876 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.53 % Favored : 87.25 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.61 % 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: -2.97 (0.09), residues: 6650 helix: -0.70 (0.11), residues: 2058 sheet: -1.89 (0.17), residues: 776 loop : -2.86 (0.09), residues: 3816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 795 time to evaluate : 6.499 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 outliers start: 134 outliers final: 71 residues processed: 873 average time/residue: 1.2165 time to fit residues: 1912.9404 Evaluate side-chains 785 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 714 time to evaluate : 6.422 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 71 outliers final: 2 residues processed: 71 average time/residue: 1.1124 time to fit residues: 153.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 606 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 585 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 189 optimal weight: 0.0040 chunk 623 optimal weight: 2.9990 chunk 667 optimal weight: 10.0000 chunk 484 optimal weight: 0.0770 chunk 91 optimal weight: 20.0000 chunk 770 optimal weight: 10.0000 overall best weight: 2.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 48 GLN C 279 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS L 99 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 HIS ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 145 GLN a 148 HIS ** b 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 393 HIS ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 1.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.906 139014 Z= 0.610 Angle : 0.927 45.384 204868 Z= 0.467 Chirality : 0.049 2.006 25744 Planarity : 0.006 0.185 12919 Dihedral : 18.342 179.670 49876 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.76 % Favored : 88.11 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.61 % 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: -2.62 (0.10), residues: 6650 helix: -0.35 (0.11), residues: 2060 sheet: -1.69 (0.18), residues: 748 loop : -2.68 (0.09), residues: 3842 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 870 time to evaluate : 6.474 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 outliers start: 90 outliers final: 35 residues processed: 919 average time/residue: 1.1297 time to fit residues: 1823.3629 Evaluate side-chains 778 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 743 time to evaluate : 5.947 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 2 residues processed: 35 average time/residue: 0.9507 time to fit residues: 68.4491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 891 optimal weight: 9.9990 chunk 939 optimal weight: 10.0000 chunk 856 optimal weight: 20.0000 chunk 913 optimal weight: 20.0000 chunk 938 optimal weight: 20.0000 chunk 549 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 717 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 825 optimal weight: 20.0000 chunk 863 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 HIS A 194 ASN B 3 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 305 ASN D 534 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 GLN T 16 GLN ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN U 166 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 HIS e 250 ASN ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 32 ASN ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 1.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.885 139014 Z= 0.679 Angle : 1.043 46.185 204868 Z= 0.525 Chirality : 0.054 1.878 25744 Planarity : 0.007 0.115 12919 Dihedral : 18.855 179.778 49876 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 40.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.08 % Favored : 85.76 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.51 % 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: -2.97 (0.09), residues: 6650 helix: -0.69 (0.11), residues: 2028 sheet: -1.79 (0.18), residues: 711 loop : -2.87 (0.09), residues: 3911 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 736 time to evaluate : 6.427 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: 111 outliers final: 58 residues processed: 794 average time/residue: 1.2137 time to fit residues: 1708.9828 Evaluate side-chains 741 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 683 time to evaluate : 6.387 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 58 outliers final: 2 residues processed: 58 average time/residue: 1.1411 time to fit residues: 125.9862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 910 optimal weight: 20.0000 chunk 599 optimal weight: 6.9990 chunk 965 optimal weight: 20.0000 chunk 589 optimal weight: 7.9990 chunk 458 optimal weight: 5.9990 chunk 671 optimal weight: 10.0000 chunk 1013 optimal weight: 40.0000 chunk 932 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 623 optimal weight: 0.0770 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 HIS ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 1.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.900 139014 Z= 0.634 Angle : 0.978 45.911 204868 Z= 0.494 Chirality : 0.052 1.933 25744 Planarity : 0.006 0.098 12919 Dihedral : 18.593 179.923 49876 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.95 % Favored : 86.92 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -2.86 (0.10), residues: 6650 helix: -0.60 (0.11), residues: 2044 sheet: -1.78 (0.18), residues: 756 loop : -2.79 (0.09), residues: 3850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13300 Ramachandran restraints generated. 6650 Oldfield, 0 Emsley, 6650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 750 time to evaluate : 6.519 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: 50 outliers final: 32 residues processed: 771 average time/residue: 1.1039 time to fit residues: 1538.8753 Evaluate side-chains 727 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 695 time to evaluate : 6.372 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 3 residues processed: 32 average time/residue: 1.0349 time to fit residues: 68.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 494 optimal weight: 20.0000 chunk 640 optimal weight: 3.9990 chunk 859 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 743 optimal weight: 20.0000 chunk 119 optimal weight: 0.0770 chunk 224 optimal weight: 6.9990 chunk 808 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 829 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 HIS ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 229 ASN f 360 GLN ** f 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.053019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.042242 restraints weight = 1380766.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.042848 restraints weight = 527815.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.043329 restraints weight = 271614.394| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 1.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.856 139014 Z= 0.621 Angle : 0.958 45.615 204868 Z= 0.483 Chirality : 0.050 2.086 25744 Planarity : 0.006 0.145 12919 Dihedral : 18.424 179.598 49876 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 32.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.67 % Favored : 86.21 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -2.80 (0.10), residues: 6650 helix: -0.51 (0.11), residues: 2034 sheet: -1.76 (0.17), residues: 780 loop : -2.77 (0.09), residues: 3836 =============================================================================== Job complete usr+sys time: 32454.93 seconds wall clock time: 571 minutes 16.73 seconds (34276.73 seconds total)