Starting phenix.real_space_refine on Fri Mar 15 20:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/03_2024/6oig_20077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/03_2024/6oig_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_20077/03_2024/6oig_20077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/03_2024/6oig_20077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/03_2024/6oig_20077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oig_20077/03_2024/6oig_20077.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5265/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: 3 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: 47.66, per 1000 atoms: 0.37 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: 72.06 Conformation dependent library (CDL) restraints added in 7.1 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: 45.72 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: 177.96 Time building geometry restraints manager: 75.90 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: 76528 35.97 - 71.93: 10589 71.93 - 107.90: 1072 107.90 - 143.86: 29 143.86 - 179.83: 39 Dihedral angle restraints: 88257 sinusoidal: 68400 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 88254 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: 2.310 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: 0.100 Extract box with map and model: 15.590 Check model and map are aligned: 1.400 Set scattering table: 0.880 Process input model: 434.050 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.330 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:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 459.440 ------------------------------------------------------------------------------- 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 : 24.979 179.827 75435 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 % Allowed : 5.76 % Favored : 93.05 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 194 HIS 0.028 0.004 HIS T 22 PHE 0.051 0.005 PHE B 199 TYR 0.048 0.005 TYR f 371 ARG 0.028 0.002 ARG P 171 *********************** 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 : 6.123 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 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 271 ASN cc_start: 0.8875 (m-40) cc_final: 0.8607 (m110) REVERT: F 274 GLN cc_start: 0.8433 (tp40) cc_final: 0.8209 (tp-100) REVERT: F 292 LYS cc_start: 0.6970 (ptmt) cc_final: 0.6303 (mmtp) REVERT: F 327 VAL cc_start: 0.8529 (t) cc_final: 0.8187 (t) REVERT: G 226 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8041 (mmtt) REVERT: G 321 VAL cc_start: 0.7136 (t) cc_final: 0.6841 (p) REVERT: H 238 LEU cc_start: 0.8148 (mt) cc_final: 0.7577 (mp) REVERT: H 286 TYR cc_start: 0.6148 (m-80) cc_final: 0.5865 (m-80) REVERT: H 379 ILE cc_start: 0.6455 (mt) cc_final: 0.6211 (tp) REVERT: I 233 LEU cc_start: 0.4026 (OUTLIER) cc_final: 0.3480 (tm) REVERT: I 234 CYS cc_start: 0.1672 (t) cc_final: 0.1398 (t) REVERT: I 298 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6427 (tm-30) REVERT: I 350 ILE cc_start: 0.2216 (pt) cc_final: 0.1729 (pt) REVERT: L 92 THR cc_start: 0.7496 (p) cc_final: 0.7267 (p) REVERT: M 189 ASP cc_start: 0.4952 (p0) cc_final: 0.4637 (p0) REVERT: O 8 VAL cc_start: 0.8775 (t) cc_final: 0.8159 (t) REVERT: O 27 LEU cc_start: 0.7588 (mt) cc_final: 0.7069 (mt) REVERT: P 112 LEU cc_start: 0.9435 (tp) cc_final: 0.9156 (tp) REVERT: P 129 THR cc_start: 0.8403 (m) cc_final: 0.8182 (p) REVERT: Q 239 ILE cc_start: 0.7724 (mt) cc_final: 0.7232 (mt) REVERT: R 167 ILE cc_start: 0.8816 (mt) cc_final: 0.8536 (mm) REVERT: R 171 ASN cc_start: 0.5738 (p0) cc_final: 0.5113 (t0) REVERT: R 239 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (ptt-90) REVERT: R 240 LEU cc_start: 0.9159 (tt) cc_final: 0.8804 (mt) REVERT: R 261 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8545 (mm-30) REVERT: S 4 PHE cc_start: 0.8065 (m-80) cc_final: 0.6858 (m-80) REVERT: S 162 THR cc_start: 0.5073 (p) cc_final: 0.4677 (p) REVERT: U 174 PHE cc_start: 0.4925 (t80) cc_final: 0.4647 (t80) REVERT: V 156 ASP cc_start: 0.5019 (p0) cc_final: 0.4706 (p0) REVERT: V 174 ARG cc_start: 0.3904 (tpt170) cc_final: 0.3559 (mpp80) REVERT: V 188 MET cc_start: 0.8688 (mmp) cc_final: 0.7873 (mtt) REVERT: V 206 ILE cc_start: 0.9329 (mt) cc_final: 0.8743 (tp) REVERT: V 222 LEU cc_start: 0.4806 (pt) cc_final: 0.4312 (pt) REVERT: Z 41 LEU cc_start: 0.9450 (mp) cc_final: 0.9178 (mm) REVERT: Z 67 ILE cc_start: 0.8390 (mt) cc_final: 0.7739 (mt) REVERT: Z 70 PHE cc_start: 0.7337 (p90) cc_final: 0.6930 (p90) REVERT: Z 86 LEU cc_start: 0.7946 (tp) cc_final: 0.7653 (tt) REVERT: Z 91 PHE cc_start: 0.9127 (m-80) cc_final: 0.8439 (m-80) REVERT: c 65 THR cc_start: 0.7493 (m) cc_final: 0.7263 (m) REVERT: c 68 TYR cc_start: 0.7685 (t80) cc_final: 0.7213 (t80) REVERT: d 131 LEU cc_start: 0.8361 (mt) cc_final: 0.8145 (mt) REVERT: d 147 LEU cc_start: 0.8547 (mt) cc_final: 0.8278 (mt) REVERT: e 169 LYS cc_start: 0.7418 (mttt) cc_final: 0.7183 (mtmm) REVERT: e 179 VAL cc_start: 0.8145 (t) cc_final: 0.7725 (t) REVERT: e 226 LEU cc_start: 0.6307 (mt) cc_final: 0.5593 (tp) REVERT: f 325 LEU cc_start: 0.7488 (mt) cc_final: 0.7254 (mp) REVERT: f 336 ARG cc_start: 0.6521 (ptm160) cc_final: 0.5220 (ptp90) REVERT: f 342 ASN cc_start: 0.6259 (t0) cc_final: 0.5502 (t0) REVERT: f 363 LEU cc_start: 0.5517 (mt) cc_final: 0.5315 (mt) REVERT: f 369 TYR cc_start: 0.7962 (t80) cc_final: 0.7578 (t80) REVERT: f 402 THR cc_start: 0.6919 (p) cc_final: 0.6366 (p) REVERT: g 101 VAL cc_start: 0.9368 (t) cc_final: 0.9145 (t) REVERT: h 33 VAL cc_start: 0.8569 (t) cc_final: 0.8176 (p) REVERT: h 57 VAL cc_start: 0.9241 (t) cc_final: 0.8802 (t) REVERT: h 96 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8651 (tt0) REVERT: h 99 GLN cc_start: 0.7855 (mm110) cc_final: 0.7571 (mm-40) REVERT: i 98 ARG cc_start: 0.7573 (tpp80) cc_final: 0.7192 (tpt170) REVERT: k 32 ASN cc_start: 0.5963 (p0) cc_final: 0.5679 (p0) REVERT: l 5 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.5491 (pttm) REVERT: m 106 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8196 (ttt-90) REVERT: o 53 GLN cc_start: 0.7163 (tp40) cc_final: 0.6000 (tm-30) REVERT: p 26 VAL cc_start: 0.8991 (t) cc_final: 0.8728 (m) REVERT: p 54 ILE cc_start: 0.6780 (mt) cc_final: 0.6478 (mp) REVERT: p 71 VAL cc_start: 0.5956 (t) cc_final: 0.5298 (m) outliers start: 66 outliers final: 15 residues processed: 1939 average time/residue: 1.2324 time to fit residues: 3962.1170 Evaluate side-chains 982 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 963 time to evaluate : 6.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 344 THR Chi-restraints excluded: chain z residue 360 LEU Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 256 LYS Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 232 ARG Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain q residue 84 VAL 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 335 HIS ** z 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN F 271 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 277 ASN H 316 ASN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 ASN ** 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** J 98 ASN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN L 102 GLN ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** N 86 ASN ** 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 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 ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** Z 126 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 360 GLN ** f 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 14 ASN 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 ** h 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN i 92 ASN ** j 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 ASN ** o 22 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: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.895 139014 Z= 0.839 Angle : 1.623 82.332 204868 Z= 0.774 Chirality : 0.071 2.141 25744 Planarity : 0.011 0.292 12919 Dihedral : 26.576 179.702 62160 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 55.37 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.96 % Favored : 86.21 % Rotamer: Outliers : 6.07 % Allowed : 17.46 % Favored : 76.48 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.95 % Twisted General : 1.55 % 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: -4.33 (0.09), residues: 6650 helix: -2.52 (0.09), residues: 1995 sheet: -2.98 (0.18), residues: 663 loop : -3.18 (0.09), residues: 3992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP N 200 HIS 0.029 0.003 HIS q 39 PHE 0.132 0.004 PHE N 21 TYR 0.116 0.004 TYR N 127 ARG 0.065 0.002 ARG N 24 *********************** 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 1464 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1129 time to evaluate : 6.233 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: z 280 MET cc_start: 0.3476 (mmt) cc_final: 0.2979 (mtt) REVERT: A 142 ASP cc_start: 0.4428 (t0) cc_final: 0.3857 (t0) REVERT: F 265 TYR cc_start: 0.6582 (m-80) cc_final: 0.6151 (m-80) REVERT: F 314 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8855 (mm110) REVERT: F 340 ILE cc_start: 0.8992 (pt) cc_final: 0.8617 (mt) REVERT: F 400 THR cc_start: 0.8115 (p) cc_final: 0.7426 (p) REVERT: G 244 TYR cc_start: 0.7811 (m-80) cc_final: 0.7487 (m-80) REVERT: G 343 ILE cc_start: 0.9048 (mt) cc_final: 0.8774 (mt) REVERT: H 361 LEU cc_start: 0.8621 (tp) cc_final: 0.8274 (pp) REVERT: I 198 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7183 (tttt) REVERT: I 256 CYS cc_start: 0.9296 (t) cc_final: 0.8982 (p) REVERT: I 287 MET cc_start: 0.5256 (ttp) cc_final: 0.4711 (ttp) REVERT: I 298 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6436 (tm-30) REVERT: N 7 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.5272 (tp) REVERT: N 57 GLN cc_start: 0.8882 (mt0) cc_final: 0.8566 (mp10) REVERT: O 64 PHE cc_start: 0.3816 (p90) cc_final: 0.2557 (p90) REVERT: P 31 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9196 (mm-30) REVERT: R 171 ASN cc_start: 0.6511 (p0) cc_final: 0.5691 (t0) REVERT: R 261 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8706 (mm-30) REVERT: V 188 MET cc_start: 0.8930 (mmp) cc_final: 0.8059 (mtp) REVERT: V 203 MET cc_start: 0.8531 (mtm) cc_final: 0.8103 (mpp) REVERT: V 206 ILE cc_start: 0.9281 (mt) cc_final: 0.8787 (tp) REVERT: V 227 ASN cc_start: 0.8702 (m-40) cc_final: 0.8429 (m-40) REVERT: V 238 MET cc_start: 0.7689 (mmm) cc_final: 0.6870 (mmm) REVERT: W 225 ARG cc_start: -0.1588 (OUTLIER) cc_final: -0.3145 (mmm160) REVERT: X 202 MET cc_start: 0.5688 (pmm) cc_final: 0.4228 (mmt) REVERT: Z 17 TYR cc_start: 0.8182 (m-80) cc_final: 0.7432 (m-80) REVERT: Z 46 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8314 (tm-30) REVERT: Z 70 PHE cc_start: 0.7594 (p90) cc_final: 0.6362 (p90) REVERT: Z 71 ILE cc_start: 0.8631 (pt) cc_final: 0.8314 (pt) REVERT: Z 105 GLN cc_start: 0.9268 (mt0) cc_final: 0.9054 (mt0) REVERT: Z 110 LYS cc_start: 0.8924 (mttt) cc_final: 0.8340 (ptmt) REVERT: Z 118 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8387 (mm-30) REVERT: a 122 HIS cc_start: 0.7719 (m90) cc_final: 0.7189 (m-70) REVERT: a 217 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7810 (mt-10) REVERT: c 32 LYS cc_start: 0.9509 (tptm) cc_final: 0.9245 (tppt) REVERT: c 94 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7718 (tm-30) REVERT: d 131 LEU cc_start: 0.8396 (mt) cc_final: 0.8009 (mt) REVERT: e 176 TYR cc_start: 0.6490 (m-80) cc_final: 0.6203 (m-80) REVERT: e 183 TRP cc_start: 0.8026 (t-100) cc_final: 0.7824 (t-100) REVERT: e 274 LYS cc_start: 0.6963 (mtpp) cc_final: 0.6699 (tptp) REVERT: f 390 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7506 (t) REVERT: g 7 PHE cc_start: 0.4578 (m-80) cc_final: 0.2413 (m-80) REVERT: h 30 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8994 (tp30) REVERT: i 98 ARG cc_start: 0.7518 (tpp80) cc_final: 0.6443 (tpt170) REVERT: l 5 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.5512 (pttm) REVERT: l 35 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (tt) REVERT: l 40 LYS cc_start: 0.5698 (mtpp) cc_final: 0.5482 (mtpt) REVERT: o 25 VAL cc_start: 0.7744 (t) cc_final: 0.7059 (t) REVERT: o 35 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.3831 (tp) REVERT: o 91 PHE cc_start: 0.7199 (p90) cc_final: 0.6942 (p90) outliers start: 335 outliers final: 187 residues processed: 1356 average time/residue: 1.1138 time to fit residues: 2585.8135 Evaluate side-chains 1010 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 817 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 212 LEU Chi-restraints excluded: chain z residue 214 TYR Chi-restraints excluded: chain z residue 219 LYS Chi-restraints excluded: chain z residue 220 LYS Chi-restraints excluded: chain z residue 225 GLU Chi-restraints excluded: chain z residue 258 MET Chi-restraints excluded: chain z residue 260 ILE Chi-restraints excluded: chain z residue 344 THR Chi-restraints excluded: chain z residue 360 LEU Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 106 TRP Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 363 GLN Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 320 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 17 HIS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 180 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 148 LYS Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain Q residue 135 HIS Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain U residue 129 LEU Chi-restraints excluded: chain U residue 175 VAL Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 148 VAL Chi-restraints excluded: chain V residue 151 ILE Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 220 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 225 ARG Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 213 VAL Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 126 ASN Chi-restraints excluded: chain a residue 96 VAL Chi-restraints excluded: chain a residue 121 HIS Chi-restraints excluded: chain a residue 129 TYR Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 249 HIS Chi-restraints excluded: chain f residue 327 VAL Chi-restraints excluded: chain f residue 339 ARG Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 374 SER Chi-restraints excluded: chain f residue 390 THR Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain f residue 421 TYR Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 815 VAL Chi-restraints excluded: chain j residue 830 THR Chi-restraints excluded: chain j residue 850 MET Chi-restraints excluded: chain j residue 856 VAL Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain o residue 32 LYS Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 37 GLN Chi-restraints excluded: chain q residue 38 MET Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain q residue 53 MET Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 66 PHE Chi-restraints excluded: chain q residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 768 optimal weight: 10.0000 chunk 628 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 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: 20.0000 chunk 742 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 392 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** 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 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** H 250 ASN ** H 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 ASN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 ASN ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 GLN J 181 GLN L 17 HIS M 205 GLN ** 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS P 50 GLN P 54 HIS ** 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** R 279 GLN ** 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 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 ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 194 ASN ** 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 ** 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 406 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 HIS g 61 GLN h 59 ASN ** 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN l 25 GLN ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 37 GLN ** 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.869 139014 Z= 0.720 Angle : 1.227 61.563 204868 Z= 0.606 Chirality : 0.057 1.953 25744 Planarity : 0.009 0.154 12919 Dihedral : 25.706 179.529 62144 Min Nonbonded Distance : 1.272 Molprobity Statistics. All-atom Clashscore : 41.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 12.42 % Favored : 86.98 % Rotamer: Outliers : 6.85 % Allowed : 20.12 % Favored : 73.04 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % Twisted General : 1.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.09), residues: 6650 helix: -1.64 (0.10), residues: 2020 sheet: -2.67 (0.17), residues: 727 loop : -3.04 (0.09), residues: 3903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP V 214 HIS 0.030 0.002 HIS q 39 PHE 0.050 0.003 PHE z 223 TYR 0.070 0.003 TYR N 4 ARG 0.025 0.001 ARG q 46 *********************** 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 1405 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1027 time to evaluate : 6.329 Fit side-chains 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: z 260 ILE cc_start: 0.0224 (OUTLIER) cc_final: -0.0455 (mt) REVERT: B 66 LYS cc_start: 0.3096 (mttt) cc_final: 0.2830 (mttp) REVERT: D 363 LEU cc_start: 0.9036 (tp) cc_final: 0.8750 (mt) REVERT: F 271 ASN cc_start: 0.9261 (m110) cc_final: 0.9057 (p0) REVERT: F 314 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8685 (mp10) REVERT: F 318 LEU cc_start: 0.9184 (mm) cc_final: 0.8836 (tp) REVERT: F 340 ILE cc_start: 0.9065 (pt) cc_final: 0.8765 (mt) REVERT: G 225 GLN cc_start: 0.9309 (mt0) cc_final: 0.8882 (mt0) REVERT: G 244 TYR cc_start: 0.8365 (m-80) cc_final: 0.8018 (m-80) REVERT: H 245 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6442 (t80) REVERT: I 211 VAL cc_start: 0.3053 (m) cc_final: 0.2664 (m) REVERT: I 213 ASP cc_start: 0.6649 (m-30) cc_final: 0.5915 (t0) REVERT: I 256 CYS cc_start: 0.9204 (t) cc_final: 0.8945 (p) REVERT: I 298 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7291 (tm-30) REVERT: M 190 GLN cc_start: 0.5828 (tm-30) cc_final: 0.5627 (tm-30) REVERT: P 22 LEU cc_start: 0.8122 (mm) cc_final: 0.7885 (tp) REVERT: P 31 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9259 (mm-30) REVERT: P 37 ASN cc_start: 0.9238 (t0) cc_final: 0.8201 (m110) REVERT: P 58 ILE cc_start: 0.8653 (mm) cc_final: 0.8400 (mp) REVERT: P 79 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7647 (t) REVERT: P 107 LEU cc_start: 0.8385 (mt) cc_final: 0.8132 (mm) REVERT: P 108 ASP cc_start: 0.6124 (OUTLIER) cc_final: 0.5025 (t0) REVERT: Q 196 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6754 (mm) REVERT: R 171 ASN cc_start: 0.7470 (p0) cc_final: 0.6675 (t0) REVERT: R 207 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8377 (tp30) REVERT: R 250 ILE cc_start: 0.8660 (mp) cc_final: 0.8096 (tt) REVERT: R 261 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8720 (mm-30) REVERT: S 27 MET cc_start: 0.6141 (tpt) cc_final: 0.5919 (tpt) REVERT: S 90 MET cc_start: 0.8765 (mtp) cc_final: 0.8320 (ttm) REVERT: V 163 LEU cc_start: 0.9234 (mt) cc_final: 0.8779 (mt) REVERT: V 188 MET cc_start: 0.9091 (mmp) cc_final: 0.8279 (mtm) REVERT: V 203 MET cc_start: 0.8500 (mtm) cc_final: 0.7973 (mpp) REVERT: V 243 ILE cc_start: 0.8373 (mm) cc_final: 0.8025 (mp) REVERT: V 257 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: W 225 ARG cc_start: -0.1205 (OUTLIER) cc_final: -0.2583 (mmm-85) REVERT: X 202 MET cc_start: 0.6101 (pmm) cc_final: 0.5213 (mmp) REVERT: Z 17 TYR cc_start: 0.8507 (m-80) cc_final: 0.7717 (m-80) REVERT: Z 41 LEU cc_start: 0.9416 (mt) cc_final: 0.9107 (mm) REVERT: Z 68 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7702 (mtpp) REVERT: Z 70 PHE cc_start: 0.7926 (p90) cc_final: 0.5799 (p90) REVERT: Z 71 ILE cc_start: 0.8928 (pt) cc_final: 0.8504 (pt) REVERT: Z 98 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9171 (tt0) REVERT: Z 105 GLN cc_start: 0.9332 (mt0) cc_final: 0.9019 (mt0) REVERT: Z 110 LYS cc_start: 0.9103 (mttt) cc_final: 0.8836 (ptpp) REVERT: Z 118 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8431 (mm-30) REVERT: a 123 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7500 (ttt180) REVERT: a 190 TYR cc_start: 0.7835 (m-10) cc_final: 0.7603 (m-10) REVERT: c 68 TYR cc_start: 0.9065 (t80) cc_final: 0.8851 (t80) REVERT: c 94 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8267 (tm-30) REVERT: e 160 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8401 (mm) REVERT: e 183 TRP cc_start: 0.7798 (t-100) cc_final: 0.7585 (t-100) REVERT: g 13 TYR cc_start: 0.8304 (m-10) cc_final: 0.7537 (m-10) REVERT: g 33 GLN cc_start: 0.5736 (pp30) cc_final: 0.5474 (pm20) REVERT: h 30 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8856 (tp30) REVERT: i 98 ARG cc_start: 0.7354 (tpp80) cc_final: 0.7011 (tpt170) REVERT: j 833 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.4987 (m-80) REVERT: k 38 PHE cc_start: 0.5853 (p90) cc_final: 0.5332 (p90) REVERT: l 37 TYR cc_start: 0.6643 (p90) cc_final: 0.6057 (p90) REVERT: m 103 LEU cc_start: 0.8388 (mm) cc_final: 0.7745 (mp) REVERT: p 32 GLN cc_start: 0.7789 (mt0) cc_final: 0.7469 (tp-100) REVERT: p 37 TYR cc_start: 0.7637 (m-10) cc_final: 0.7413 (m-10) REVERT: q 52 LEU cc_start: 0.6240 (mt) cc_final: 0.5929 (mt) outliers start: 378 outliers final: 219 residues processed: 1286 average time/residue: 1.2245 time to fit residues: 2726.4760 Evaluate side-chains 1041 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 811 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 214 TYR Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 252 ASN Chi-restraints excluded: chain z residue 260 ILE Chi-restraints excluded: chain z residue 344 THR Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 371 GLU Chi-restraints excluded: chain z residue 376 ASN Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 106 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 245 PHE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 320 ILE Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 243 HIS Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 HIS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 205 GLN Chi-restraints excluded: chain M residue 242 LYS Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 26 ARG Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 72 LYS Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 246 CYS Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 81 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 163 PHE Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain U residue 145 VAL Chi-restraints excluded: chain U residue 175 VAL Chi-restraints excluded: chain V residue 148 VAL Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 220 VAL Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 150 ILE Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 225 ARG Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 188 LYS Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 205 ASN Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 68 LYS Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 98 GLU Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 44 ILE Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 229 ASN Chi-restraints excluded: chain f residue 327 VAL Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 402 THR Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain j residue 830 THR Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 847 THR Chi-restraints excluded: chain j residue 850 MET Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain m residue 126 LYS Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain q residue 57 THR 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: 20.0000 chunk 480 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 441 optimal weight: 0.6980 chunk 621 optimal weight: 3.9990 chunk 928 optimal weight: 20.0000 chunk 983 optimal weight: 10.0000 chunk 485 optimal weight: 7.9990 chunk 880 optimal weight: 20.0000 chunk 264 optimal weight: 40.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- 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 ** z 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN G 259 ASN 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 277 HIS ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 25 HIS ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN Q 198 GLN Q 270 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 GLN ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 261 ASN ** 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** ** Z 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** 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 109 HIS d 115 GLN g 14 ASN h 59 ASN h 62 GLN h 76 GLN ** 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 57 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.869 139014 Z= 0.696 Angle : 1.126 57.129 204868 Z= 0.562 Chirality : 0.056 1.941 25744 Planarity : 0.008 0.125 12919 Dihedral : 25.396 179.781 62136 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 40.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.01 % Favored : 86.62 % Rotamer: Outliers : 7.17 % Allowed : 21.70 % Favored : 71.13 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.34 % Twisted General : 0.79 % 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: -3.46 (0.09), residues: 6650 helix: -1.22 (0.11), residues: 2026 sheet: -2.50 (0.17), residues: 736 loop : -3.00 (0.09), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP V 214 HIS 0.046 0.002 HIS L 17 PHE 0.042 0.003 PHE z 409 TYR 0.055 0.003 TYR N 119 ARG 0.039 0.001 ARG q 61 *********************** 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 1323 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 927 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 405 MET cc_start: 0.1826 (OUTLIER) cc_final: 0.1394 (mpp) REVERT: A 237 LEU cc_start: 0.5238 (mp) cc_final: 0.5021 (mp) REVERT: B 218 ILE cc_start: 0.5658 (mt) cc_final: 0.5257 (mt) REVERT: C 106 TRP cc_start: 0.4952 (OUTLIER) cc_final: 0.4532 (p90) REVERT: F 271 ASN cc_start: 0.9318 (m110) cc_final: 0.9092 (m-40) REVERT: F 428 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.3627 (tpt90) REVERT: G 191 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6601 (p) REVERT: G 225 GLN cc_start: 0.9231 (mt0) cc_final: 0.8862 (mt0) REVERT: G 244 TYR cc_start: 0.8888 (m-80) cc_final: 0.8353 (m-80) REVERT: H 380 TYR cc_start: 0.8150 (m-80) cc_final: 0.7937 (m-80) REVERT: H 391 LEU cc_start: 0.7149 (mt) cc_final: 0.6821 (mp) REVERT: I 213 ASP cc_start: 0.8080 (m-30) cc_final: 0.7487 (t0) REVERT: I 256 CYS cc_start: 0.9354 (t) cc_final: 0.9114 (p) REVERT: I 298 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7458 (tm-30) REVERT: I 401 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: L 102 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6468 (tp-100) REVERT: N 135 VAL cc_start: -0.2333 (OUTLIER) cc_final: -0.2559 (p) REVERT: P 21 TYR cc_start: 0.7787 (m-80) cc_final: 0.7584 (m-80) REVERT: P 26 PHE cc_start: 0.8004 (t80) cc_final: 0.7609 (t80) REVERT: P 30 ARG cc_start: 0.8076 (tmt170) cc_final: 0.7837 (tpt90) REVERT: P 31 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9126 (mm-30) REVERT: P 37 ASN cc_start: 0.9325 (t0) cc_final: 0.8370 (m-40) REVERT: P 58 ILE cc_start: 0.8775 (mm) cc_final: 0.8016 (tt) REVERT: P 79 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7736 (t) REVERT: P 105 LYS cc_start: 0.4897 (mttt) cc_final: 0.4554 (mttm) REVERT: P 108 ASP cc_start: 0.6537 (m-30) cc_final: 0.5723 (t0) REVERT: R 207 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8481 (tp30) REVERT: R 261 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8836 (mm-30) REVERT: S 36 ILE cc_start: 0.9138 (mt) cc_final: 0.8910 (mt) REVERT: S 90 MET cc_start: 0.8817 (mtp) cc_final: 0.8332 (ttm) REVERT: V 152 MET cc_start: 0.8580 (ttp) cc_final: 0.8324 (ttp) REVERT: V 188 MET cc_start: 0.9112 (mmp) cc_final: 0.8595 (mmm) REVERT: V 203 MET cc_start: 0.8722 (mtm) cc_final: 0.8157 (mpp) REVERT: V 206 ILE cc_start: 0.9311 (mp) cc_final: 0.8814 (tp) REVERT: V 235 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8135 (mmtm) REVERT: V 237 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8146 (mm-30) REVERT: V 257 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8278 (mtm-85) REVERT: W 225 ARG cc_start: -0.0760 (OUTLIER) cc_final: -0.2324 (mmm-85) REVERT: X 169 ASN cc_start: 0.5209 (t0) cc_final: 0.4650 (t0) REVERT: X 202 MET cc_start: 0.6182 (pmm) cc_final: 0.5853 (mmp) REVERT: Z 17 TYR cc_start: 0.8703 (m-80) cc_final: 0.7818 (m-80) REVERT: Z 41 LEU cc_start: 0.9458 (mt) cc_final: 0.9171 (mm) REVERT: Z 70 PHE cc_start: 0.8336 (p90) cc_final: 0.7076 (p90) REVERT: Z 87 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8796 (t0) REVERT: Z 98 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9094 (pt0) REVERT: Z 105 GLN cc_start: 0.9250 (mt0) cc_final: 0.8912 (mt0) REVERT: Z 114 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8757 (ptmm) REVERT: Z 118 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8734 (mm-30) REVERT: b 76 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6266 (t-90) REVERT: b 125 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7152 (mtmm) REVERT: c 68 TYR cc_start: 0.8891 (t80) cc_final: 0.8412 (t80) REVERT: c 94 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8652 (tm-30) REVERT: d 132 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7973 (tpt-90) REVERT: e 160 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8717 (mm) REVERT: e 183 TRP cc_start: 0.7930 (t-100) cc_final: 0.7727 (t-100) REVERT: g 13 TYR cc_start: 0.8216 (m-10) cc_final: 0.7619 (m-10) REVERT: g 14 ASN cc_start: 0.6566 (t0) cc_final: 0.6262 (t0) REVERT: g 33 GLN cc_start: 0.5629 (pp30) cc_final: 0.5375 (pm20) REVERT: g 95 ILE cc_start: 0.8419 (tp) cc_final: 0.8131 (tt) REVERT: h 30 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8710 (tp30) REVERT: i 98 ARG cc_start: 0.7364 (tpp80) cc_final: 0.6840 (tpt170) REVERT: l 37 TYR cc_start: 0.7172 (p90) cc_final: 0.6835 (p90) REVERT: m 103 LEU cc_start: 0.8538 (mm) cc_final: 0.7870 (mp) REVERT: o 90 HIS cc_start: 0.5822 (OUTLIER) cc_final: 0.5445 (t-90) REVERT: p 32 GLN cc_start: 0.8265 (mt0) cc_final: 0.7977 (tp-100) outliers start: 396 outliers final: 245 residues processed: 1207 average time/residue: 1.1139 time to fit residues: 2330.3295 Evaluate side-chains 1025 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 763 time to evaluate : 6.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 405 MET Chi-restraints excluded: chain z residue 409 PHE Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 6 TYR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 106 TRP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 360 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 245 PHE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 277 HIS Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 320 ILE Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain M residue 265 GLU Chi-restraints excluded: chain N residue 6 TYR Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 50 ASN Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 275 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain U residue 128 ASN Chi-restraints excluded: chain U residue 145 VAL Chi-restraints excluded: chain U residue 175 VAL Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 148 VAL Chi-restraints excluded: chain V residue 154 CYS Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 220 VAL Chi-restraints excluded: chain V residue 253 ASP Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 225 ARG Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 98 GLU Chi-restraints excluded: chain Z residue 114 LYS Chi-restraints excluded: chain Z residue 126 ASN Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 76 HIS Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 44 ILE Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 132 ARG Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 249 HIS Chi-restraints excluded: chain f residue 327 VAL Chi-restraints excluded: chain f residue 332 LEU Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain j residue 825 TYR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 90 HIS Chi-restraints excluded: chain o residue 92 GLU Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 30 GLU Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain q residue 61 ARG Chi-restraints excluded: chain q residue 66 PHE 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: 9.9990 chunk 14 optimal weight: 50.0000 chunk 731 optimal weight: 20.0000 chunk 405 optimal weight: 0.6980 chunk 838 optimal weight: 10.0000 chunk 679 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 6.9990 chunk 882 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 222 ASN ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** 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 ** 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 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN F 247 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 HIS ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 GLN ** 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 149 GLN ** 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 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 208 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** ** a 120 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** d 115 GLN ** e 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN ** 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 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 GLN ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.861 139014 Z= 0.682 Angle : 1.086 56.119 204868 Z= 0.542 Chirality : 0.053 1.874 25744 Planarity : 0.007 0.142 12919 Dihedral : 25.197 179.773 62135 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 40.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.37 % Favored : 86.30 % Rotamer: Outliers : 7.39 % Allowed : 23.74 % Favored : 68.87 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.17 % 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: -3.32 (0.09), residues: 6650 helix: -1.01 (0.11), residues: 2037 sheet: -2.31 (0.18), residues: 715 loop : -2.99 (0.09), residues: 3898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP j 835 HIS 0.023 0.002 HIS I 277 PHE 0.058 0.003 PHE N 21 TYR 0.052 0.003 TYR N 119 ARG 0.031 0.001 ARG q 61 *********************** 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 1265 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 408 poor density : 857 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 300 LYS cc_start: -0.4138 (OUTLIER) cc_final: -0.4972 (tttt) REVERT: z 369 MET cc_start: 0.8455 (ppp) cc_final: 0.7940 (pmm) REVERT: z 405 MET cc_start: 0.2036 (mpp) cc_final: 0.1399 (mpp) REVERT: A 237 LEU cc_start: 0.5622 (mp) cc_final: 0.5407 (mp) REVERT: C 106 TRP cc_start: 0.5226 (OUTLIER) cc_final: 0.4813 (p90) REVERT: F 428 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.4123 (tpt90) REVERT: G 191 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.6967 (p) REVERT: G 242 PHE cc_start: 0.8913 (m-80) cc_final: 0.8535 (m-80) REVERT: G 244 TYR cc_start: 0.8968 (m-80) cc_final: 0.8412 (m-80) REVERT: G 324 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8804 (mp) REVERT: H 234 LEU cc_start: 0.6143 (mt) cc_final: 0.5080 (mp) REVERT: H 278 MET cc_start: 0.9651 (ptt) cc_final: 0.9331 (tmm) REVERT: H 391 LEU cc_start: 0.7191 (mt) cc_final: 0.6935 (mp) REVERT: I 213 ASP cc_start: 0.8432 (m-30) cc_final: 0.7818 (t0) REVERT: I 256 CYS cc_start: 0.9485 (t) cc_final: 0.9279 (p) REVERT: I 270 PHE cc_start: 0.9013 (p90) cc_final: 0.8561 (p90) REVERT: I 401 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: N 170 LYS cc_start: 0.0581 (OUTLIER) cc_final: -0.1443 (mmtt) REVERT: O 106 GLU cc_start: 0.7334 (mp0) cc_final: 0.7110 (mp0) REVERT: P 21 TYR cc_start: 0.7937 (m-80) cc_final: 0.7717 (m-80) REVERT: P 26 PHE cc_start: 0.7946 (t80) cc_final: 0.7744 (t80) REVERT: P 31 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9171 (mm-30) REVERT: P 37 ASN cc_start: 0.9386 (t0) cc_final: 0.8338 (m-40) REVERT: P 58 ILE cc_start: 0.8844 (mm) cc_final: 0.8558 (mp) REVERT: P 79 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7816 (t) REVERT: P 108 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6153 (t0) REVERT: P 147 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6560 (tp30) REVERT: P 155 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: R 230 TRP cc_start: 0.8434 (t-100) cc_final: 0.8056 (t-100) REVERT: R 261 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8887 (mm-30) REVERT: S 90 MET cc_start: 0.8809 (mtp) cc_final: 0.8355 (ttm) REVERT: T 128 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5614 (mt) REVERT: V 188 MET cc_start: 0.9141 (mmp) cc_final: 0.8778 (mmm) REVERT: V 203 MET cc_start: 0.8937 (mtm) cc_final: 0.8326 (mpp) REVERT: V 206 ILE cc_start: 0.9264 (mp) cc_final: 0.8686 (tp) REVERT: V 225 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7566 (pp20) REVERT: V 235 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8413 (mmtm) REVERT: V 237 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8288 (mm-30) REVERT: W 225 ARG cc_start: -0.0741 (OUTLIER) cc_final: -0.2205 (mmm-85) REVERT: Z 46 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9045 (pp20) REVERT: Z 70 PHE cc_start: 0.8448 (p90) cc_final: 0.7911 (p90) REVERT: Z 105 GLN cc_start: 0.9197 (mt0) cc_final: 0.8945 (mt0) REVERT: Z 118 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8726 (mm-30) REVERT: a 123 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7687 (ttp-170) REVERT: c 94 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8625 (tm-30) REVERT: d 152 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8471 (pm20) REVERT: e 160 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8674 (mm) REVERT: e 202 SER cc_start: 0.9158 (m) cc_final: 0.8679 (p) REVERT: f 376 GLU cc_start: 0.7311 (tt0) cc_final: 0.7108 (tt0) REVERT: g 6 THR cc_start: 0.4472 (p) cc_final: 0.4111 (p) REVERT: g 13 TYR cc_start: 0.8049 (m-80) cc_final: 0.7465 (m-10) REVERT: g 33 GLN cc_start: 0.6054 (pp30) cc_final: 0.5742 (pm20) REVERT: h 30 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8672 (tp30) REVERT: h 59 ASN cc_start: 0.7905 (t0) cc_final: 0.7703 (t0) REVERT: i 98 ARG cc_start: 0.7240 (tpp80) cc_final: 0.6771 (tpt170) REVERT: j 830 THR cc_start: 0.6949 (m) cc_final: 0.6708 (m) REVERT: j 833 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.4888 (m-80) REVERT: l 37 TYR cc_start: 0.7880 (p90) cc_final: 0.7446 (p90) REVERT: l 40 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8664 (mptt) REVERT: m 103 LEU cc_start: 0.8644 (mm) cc_final: 0.7951 (mp) REVERT: o 90 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5911 (t-90) REVERT: p 37 TYR cc_start: 0.7891 (m-10) cc_final: 0.7612 (m-10) REVERT: p 89 MET cc_start: 0.8941 (tpp) cc_final: 0.8676 (ptp) REVERT: q 22 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5800 (m-80) outliers start: 408 outliers final: 270 residues processed: 1149 average time/residue: 1.1007 time to fit residues: 2201.3090 Evaluate side-chains 1027 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 739 time to evaluate : 6.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 362 VAL Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 106 TRP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 245 PHE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 363 GLN Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 344 PHE Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 HIS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain N residue 6 TYR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 192 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 50 ASN Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 155 GLU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 275 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 128 ASN Chi-restraints excluded: chain U residue 170 ASP Chi-restraints excluded: chain U residue 175 VAL Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 148 VAL Chi-restraints excluded: chain V residue 154 CYS Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 253 ASP Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 225 ARG Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 150 LYS Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 220 ASP Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 247 LEU Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 126 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 129 TYR Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 44 ILE Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain f residue 327 VAL Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 391 ARG Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 825 TYR Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain o residue 48 SER Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 90 HIS Chi-restraints excluded: chain o residue 92 GLU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 30 GLU Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 22 TYR Chi-restraints excluded: chain q residue 53 MET Chi-restraints excluded: chain q residue 66 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 5.9990 chunk 885 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 577 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 983 optimal weight: 10.0000 chunk 816 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 516 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 235 ASN z 383 ASN A 132 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** B 184 ASN ** 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 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS D 305 ASN ** E 228 GLN ** 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 274 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 HIS H 363 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 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 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 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 261 ASN ** X 199 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** f 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 67 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 82 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.9768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.887 139014 Z= 0.643 Angle : 1.009 55.838 204868 Z= 0.505 Chirality : 0.051 1.892 25744 Planarity : 0.007 0.139 12919 Dihedral : 24.943 179.922 62133 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 34.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.35 % Favored : 87.41 % Rotamer: Outliers : 6.21 % Allowed : 25.57 % Favored : 68.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.68 % 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: -3.04 (0.09), residues: 6650 helix: -0.73 (0.11), residues: 2043 sheet: -2.23 (0.17), residues: 754 loop : -2.83 (0.09), residues: 3853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP U 171 HIS 0.015 0.002 HIS q 39 PHE 0.054 0.003 PHE N 21 TYR 0.072 0.003 TYR z 214 ARG 0.023 0.001 ARG N 144 *********************** 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 1190 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 847 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 300 LYS cc_start: -0.4471 (OUTLIER) cc_final: -0.5534 (tttm) REVERT: z 369 MET cc_start: 0.8664 (ppp) cc_final: 0.8109 (pmm) REVERT: z 405 MET cc_start: 0.2194 (mpp) cc_final: 0.1648 (mpp) REVERT: C 92 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5954 (p0) REVERT: C 258 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6228 (tt) REVERT: G 242 PHE cc_start: 0.8946 (m-80) cc_final: 0.8653 (m-80) REVERT: G 244 TYR cc_start: 0.9075 (m-80) cc_final: 0.8466 (m-80) REVERT: G 324 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8803 (mm) REVERT: G 391 ASP cc_start: 0.9253 (m-30) cc_final: 0.8876 (p0) REVERT: H 209 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: H 234 LEU cc_start: 0.6196 (mt) cc_final: 0.5158 (mp) REVERT: H 278 MET cc_start: 0.9622 (ptt) cc_final: 0.9215 (tmm) REVERT: I 213 ASP cc_start: 0.8558 (m-30) cc_final: 0.7956 (t0) REVERT: I 243 GLU cc_start: 0.8024 (pt0) cc_final: 0.7731 (pm20) REVERT: I 270 PHE cc_start: 0.8977 (p90) cc_final: 0.8514 (p90) REVERT: I 298 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7461 (tm-30) REVERT: N 29 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.3646 (mp0) REVERT: O 106 GLU cc_start: 0.7165 (mp0) cc_final: 0.6816 (mp0) REVERT: P 21 TYR cc_start: 0.7987 (m-80) cc_final: 0.7733 (m-80) REVERT: P 31 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9024 (mm-30) REVERT: P 37 ASN cc_start: 0.9322 (t0) cc_final: 0.8360 (m-40) REVERT: P 58 ILE cc_start: 0.8852 (mm) cc_final: 0.8587 (mp) REVERT: P 79 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8007 (t) REVERT: P 108 ASP cc_start: 0.6997 (m-30) cc_final: 0.6453 (t0) REVERT: P 155 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: R 207 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8387 (tp30) REVERT: R 230 TRP cc_start: 0.8399 (t-100) cc_final: 0.7983 (t-100) REVERT: R 261 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8862 (mm-30) REVERT: S 90 MET cc_start: 0.8800 (mtp) cc_final: 0.8349 (ttm) REVERT: T 45 ASN cc_start: 0.5233 (OUTLIER) cc_final: 0.5022 (m-40) REVERT: V 152 MET cc_start: 0.8345 (ttp) cc_final: 0.8102 (tmm) REVERT: V 174 ARG cc_start: 0.6713 (mpp80) cc_final: 0.6429 (tpt-90) REVERT: V 188 MET cc_start: 0.9147 (mmp) cc_final: 0.8621 (mtp) REVERT: V 193 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8618 (pttt) REVERT: V 203 MET cc_start: 0.8965 (mtm) cc_final: 0.8266 (mpp) REVERT: V 206 ILE cc_start: 0.9253 (mp) cc_final: 0.8816 (tp) REVERT: V 214 TRP cc_start: 0.8407 (p-90) cc_final: 0.8068 (p-90) REVERT: V 237 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8492 (mm-30) REVERT: W 208 ILE cc_start: -0.3659 (OUTLIER) cc_final: -0.3993 (pp) REVERT: W 225 ARG cc_start: -0.0944 (OUTLIER) cc_final: -0.2341 (mtt-85) REVERT: Z 70 PHE cc_start: 0.8611 (p90) cc_final: 0.7852 (p90) REVERT: Z 91 PHE cc_start: 0.9566 (m-80) cc_final: 0.9247 (m-80) REVERT: Z 105 GLN cc_start: 0.9157 (mt0) cc_final: 0.8926 (mt0) REVERT: Z 118 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8712 (mm-30) REVERT: a 115 MET cc_start: 0.5583 (mmm) cc_final: 0.5269 (mmm) REVERT: c 55 GLU cc_start: 0.9407 (pp20) cc_final: 0.9166 (pp20) REVERT: c 94 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8761 (tm-30) REVERT: d 115 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7654 (mm-40) REVERT: d 152 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8481 (pm20) REVERT: d 168 GLU cc_start: 0.9341 (pm20) cc_final: 0.9075 (pp20) REVERT: e 160 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8730 (mm) REVERT: e 165 THR cc_start: 0.8933 (p) cc_final: 0.8720 (p) REVERT: e 202 SER cc_start: 0.9257 (m) cc_final: 0.8883 (p) REVERT: f 334 TYR cc_start: 0.7762 (m-10) cc_final: 0.7237 (m-80) REVERT: f 363 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7756 (tp) REVERT: h 30 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8693 (tp30) REVERT: h 59 ASN cc_start: 0.7885 (t0) cc_final: 0.7652 (t0) REVERT: i 98 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6917 (tpt170) REVERT: j 830 THR cc_start: 0.6712 (m) cc_final: 0.6384 (m) REVERT: j 833 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: l 37 TYR cc_start: 0.8100 (p90) cc_final: 0.7686 (p90) REVERT: m 103 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8007 (mp) REVERT: o 90 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.6070 (t-90) REVERT: p 32 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7641 (tm-30) REVERT: q 52 LEU cc_start: 0.4555 (OUTLIER) cc_final: 0.3524 (tp) outliers start: 343 outliers final: 223 residues processed: 1091 average time/residue: 1.0684 time to fit residues: 2036.7187 Evaluate side-chains 992 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 751 time to evaluate : 6.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 234 LYS Chi-restraints excluded: chain z residue 299 SER Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 362 VAL Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 409 PHE Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 224 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 362 ASP Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 219 TYR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 HIS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain N residue 6 TYR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 155 GLU Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 213 THR Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 270 ASN Chi-restraints excluded: chain Q residue 275 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 81 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 154 CYS Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 190 ASN Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 225 ARG Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 150 LYS Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 83 ARG Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 44 ILE Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 226 LEU Chi-restraints excluded: chain e residue 235 THR Chi-restraints excluded: chain f residue 332 LEU Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 355 THR Chi-restraints excluded: chain f residue 363 LEU Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 825 TYR Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain o residue 48 SER Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 90 HIS Chi-restraints excluded: chain p residue 39 CYS Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 66 PHE 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: 5.9990 chunk 560 optimal weight: 5.9990 chunk 718 optimal weight: 10.0000 chunk 556 optimal weight: 6.9990 chunk 828 optimal weight: 20.0000 chunk 549 optimal weight: 9.9990 chunk 980 optimal weight: 20.0000 chunk 613 optimal weight: 7.9990 chunk 597 optimal weight: 5.9990 chunk 452 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 222 ASN ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 HIS A 97 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** 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 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** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 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** ** 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 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 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** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 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 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 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 120 HIS ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 HIS ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** o 47 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 1.0649 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= 0.665 Angle : 1.052 55.096 204868 Z= 0.525 Chirality : 0.053 1.892 25744 Planarity : 0.008 0.135 12919 Dihedral : 24.979 179.734 62132 Min Nonbonded Distance : 1.455 Molprobity Statistics. All-atom Clashscore : 40.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.88 % Favored : 85.92 % Rotamer: Outliers : 6.97 % Allowed : 26.55 % Favored : 66.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.17 % Twisted General : 0.68 % 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: -3.09 (0.09), residues: 6650 helix: -0.73 (0.11), residues: 2029 sheet: -2.12 (0.17), residues: 741 loop : -2.91 (0.09), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP N 120 HIS 0.019 0.002 HIS W 203 PHE 0.053 0.003 PHE N 21 TYR 0.051 0.003 TYR z 214 ARG 0.025 0.001 ARG l 30 *********************** 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 1182 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 797 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 369 MET cc_start: 0.8728 (ppp) cc_final: 0.8145 (pmm) REVERT: z 405 MET cc_start: 0.1938 (mpp) cc_final: 0.1414 (mpp) REVERT: C 92 ASN cc_start: 0.6362 (OUTLIER) cc_final: 0.6001 (p0) REVERT: F 295 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6680 (t80) REVERT: G 242 PHE cc_start: 0.9044 (m-80) cc_final: 0.8796 (m-80) REVERT: G 244 TYR cc_start: 0.9152 (m-80) cc_final: 0.8488 (m-80) REVERT: G 324 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8913 (mm) REVERT: G 391 ASP cc_start: 0.9300 (m-30) cc_final: 0.8918 (p0) REVERT: H 209 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: H 234 LEU cc_start: 0.6231 (mt) cc_final: 0.5217 (mp) REVERT: H 278 MET cc_start: 0.9526 (ptt) cc_final: 0.9137 (tmm) REVERT: I 213 ASP cc_start: 0.8892 (m-30) cc_final: 0.8348 (t0) REVERT: I 270 PHE cc_start: 0.9119 (p90) cc_final: 0.8741 (p90) REVERT: L 92 THR cc_start: 0.8859 (p) cc_final: 0.8630 (p) REVERT: M 209 LEU cc_start: 0.7122 (pt) cc_final: 0.6854 (pt) REVERT: N 170 LYS cc_start: 0.0539 (OUTLIER) cc_final: -0.1490 (mmtt) REVERT: O 41 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8131 (mm) REVERT: O 106 GLU cc_start: 0.6998 (mp0) cc_final: 0.6591 (mp0) REVERT: P 21 TYR cc_start: 0.8141 (m-80) cc_final: 0.7918 (m-80) REVERT: P 30 ARG cc_start: 0.8456 (tmt170) cc_final: 0.8180 (tmt170) REVERT: P 31 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8983 (mm-30) REVERT: P 37 ASN cc_start: 0.9347 (t0) cc_final: 0.8345 (m-40) REVERT: P 58 ILE cc_start: 0.8858 (mm) cc_final: 0.8596 (mp) REVERT: P 79 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7785 (t) REVERT: R 207 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8558 (tp30) REVERT: R 261 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9032 (mm-30) REVERT: S 90 MET cc_start: 0.8745 (mtp) cc_final: 0.8355 (ttm) REVERT: T 98 HIS cc_start: 0.5453 (OUTLIER) cc_final: 0.5145 (t-170) REVERT: V 188 MET cc_start: 0.9175 (mmp) cc_final: 0.8490 (mtm) REVERT: V 203 MET cc_start: 0.8948 (mtm) cc_final: 0.8275 (mpp) REVERT: V 206 ILE cc_start: 0.9298 (mp) cc_final: 0.8940 (mm) REVERT: V 249 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8691 (ptmm) REVERT: W 208 ILE cc_start: -0.3165 (OUTLIER) cc_final: -0.4044 (pp) REVERT: Z 91 PHE cc_start: 0.9588 (m-80) cc_final: 0.9053 (m-80) REVERT: Z 118 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8796 (mm-30) REVERT: c 94 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8743 (tm-30) REVERT: d 115 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8348 (mm-40) REVERT: d 152 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8368 (pm20) REVERT: d 168 GLU cc_start: 0.9186 (pm20) cc_final: 0.8864 (pp20) REVERT: e 160 ILE cc_start: 0.9412 (pt) cc_final: 0.8756 (mm) REVERT: e 189 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7689 (tp) REVERT: e 202 SER cc_start: 0.9271 (m) cc_final: 0.8977 (p) REVERT: e 246 GLU cc_start: 0.7664 (tp30) cc_final: 0.6809 (tp30) REVERT: e 247 ILE cc_start: 0.8876 (pp) cc_final: 0.8544 (pp) REVERT: f 334 TYR cc_start: 0.8207 (m-10) cc_final: 0.7994 (m-10) REVERT: f 363 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8100 (tp) REVERT: h 30 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8753 (tp30) REVERT: h 59 ASN cc_start: 0.8039 (t0) cc_final: 0.7775 (t0) REVERT: h 118 ILE cc_start: 0.6116 (mm) cc_final: 0.5910 (mm) REVERT: i 98 ARG cc_start: 0.7030 (tpp80) cc_final: 0.6490 (tpt170) REVERT: j 831 ARG cc_start: 0.4971 (OUTLIER) cc_final: 0.4756 (ttt90) REVERT: j 833 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.4768 (m-80) REVERT: l 13 MET cc_start: 0.8682 (ttt) cc_final: 0.8480 (ttt) REVERT: l 37 TYR cc_start: 0.8447 (p90) cc_final: 0.7843 (p90) REVERT: m 103 LEU cc_start: 0.8646 (mm) cc_final: 0.8007 (mp) REVERT: o 92 GLU cc_start: 0.8194 (tp30) cc_final: 0.7469 (tm-30) REVERT: o 96 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: p 32 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7867 (tm-30) outliers start: 385 outliers final: 278 residues processed: 1065 average time/residue: 1.0894 time to fit residues: 2026.3635 Evaluate side-chains 1021 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 727 time to evaluate : 6.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 299 SER Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 409 PHE Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 264 HIS Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 224 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 362 ASP Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 219 TYR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 HIS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 263 ASP Chi-restraints excluded: chain N residue 6 TYR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 62 TYR Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 159 ARG Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 275 VAL Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain R residue 244 TYR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 286 ARG Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 249 LYS Chi-restraints excluded: chain V residue 251 CYS Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 182 THR Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 240 LEU Chi-restraints excluded: chain X residue 249 ILE Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 83 ARG Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 102 ASP Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 101 HIS Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 168 PHE Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 226 LEU Chi-restraints excluded: chain e residue 258 VAL Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 347 LEU Chi-restraints excluded: chain f residue 355 THR Chi-restraints excluded: chain f residue 363 LEU Chi-restraints excluded: chain f residue 388 LYS Chi-restraints excluded: chain f residue 391 ARG Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain g residue 19 LYS Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 814 HIS Chi-restraints excluded: chain j residue 825 TYR Chi-restraints excluded: chain j residue 831 ARG Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain o residue 3 ASN Chi-restraints excluded: chain o residue 27 GLN Chi-restraints excluded: chain o residue 48 SER Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 96 GLU Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain p residue 39 CYS Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 55 LYS Chi-restraints excluded: chain q residue 60 ARG Chi-restraints excluded: chain q residue 66 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 606 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 585 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 189 optimal weight: 0.0670 chunk 623 optimal weight: 4.9990 chunk 667 optimal weight: 10.0000 chunk 484 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 770 optimal weight: 10.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 205 GLN H 209 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS O 29 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN ** 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** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN Z 77 ASN ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 HIS ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** g 108 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** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 1.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.881 139014 Z= 0.632 Angle : 0.982 55.120 204868 Z= 0.487 Chirality : 0.050 1.928 25744 Planarity : 0.006 0.086 12919 Dihedral : 24.781 179.774 62132 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 32.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.83 % Favored : 87.94 % Rotamer: Outliers : 5.32 % Allowed : 28.65 % Favored : 66.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.59 % 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: -2.84 (0.09), residues: 6650 helix: -0.47 (0.11), residues: 2039 sheet: -1.87 (0.17), residues: 766 loop : -2.83 (0.09), residues: 3845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP j 835 HIS 0.040 0.002 HIS q 39 PHE 0.045 0.002 PHE N 21 TYR 0.046 0.002 TYR z 214 ARG 0.024 0.001 ARG N 41 *********************** 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 1124 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 830 time to evaluate : 6.254 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: z 369 MET cc_start: 0.8749 (ppp) cc_final: 0.8170 (pmm) REVERT: z 405 MET cc_start: 0.2618 (OUTLIER) cc_final: 0.2169 (mpp) REVERT: F 295 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7593 (t80) REVERT: F 314 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8833 (mp10) REVERT: F 444 GLU cc_start: 0.9035 (mp0) cc_final: 0.8815 (mp0) REVERT: G 242 PHE cc_start: 0.9082 (m-80) cc_final: 0.8803 (m-80) REVERT: G 244 TYR cc_start: 0.9230 (m-80) cc_final: 0.8556 (m-80) REVERT: G 324 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8905 (mm) REVERT: G 334 CYS cc_start: 0.9096 (m) cc_final: 0.8849 (p) REVERT: G 391 ASP cc_start: 0.9296 (m-30) cc_final: 0.8935 (p0) REVERT: H 234 LEU cc_start: 0.6209 (mt) cc_final: 0.5119 (mp) REVERT: H 278 MET cc_start: 0.9530 (ptt) cc_final: 0.9144 (tmm) REVERT: I 213 ASP cc_start: 0.8980 (m-30) cc_final: 0.8436 (t0) REVERT: I 270 PHE cc_start: 0.9186 (p90) cc_final: 0.8752 (p90) REVERT: J 254 PHE cc_start: 0.4529 (t80) cc_final: 0.4187 (t80) REVERT: L 10 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.3980 (mt) REVERT: M 165 GLU cc_start: 0.3565 (OUTLIER) cc_final: 0.3195 (pt0) REVERT: N 17 ASP cc_start: 0.0082 (OUTLIER) cc_final: -0.0216 (m-30) REVERT: N 29 GLU cc_start: 0.3661 (OUTLIER) cc_final: 0.3152 (mm-30) REVERT: N 148 TYR cc_start: 0.1334 (OUTLIER) cc_final: 0.0717 (m-80) REVERT: N 170 LYS cc_start: 0.0914 (OUTLIER) cc_final: -0.1171 (mmtt) REVERT: O 27 LEU cc_start: 0.7653 (mm) cc_final: 0.7336 (mm) REVERT: O 106 GLU cc_start: 0.6890 (mp0) cc_final: 0.6518 (mp0) REVERT: O 153 VAL cc_start: 0.7477 (t) cc_final: 0.7116 (t) REVERT: P 37 ASN cc_start: 0.9365 (t0) cc_final: 0.8338 (m-40) REVERT: P 79 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7850 (t) REVERT: P 136 ILE cc_start: 0.8669 (pt) cc_final: 0.8402 (mp) REVERT: R 207 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8687 (tp30) REVERT: R 230 TRP cc_start: 0.8428 (t-100) cc_final: 0.8059 (t-100) REVERT: R 261 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8999 (mm-30) REVERT: S 90 MET cc_start: 0.8708 (mtp) cc_final: 0.8313 (ttm) REVERT: T 98 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.5195 (t-170) REVERT: T 151 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7201 (mm) REVERT: V 174 ARG cc_start: 0.6650 (tpt170) cc_final: 0.5209 (tpt-90) REVERT: V 175 LEU cc_start: 0.7709 (pp) cc_final: 0.7446 (tt) REVERT: V 188 MET cc_start: 0.9184 (mmp) cc_final: 0.8585 (mtm) REVERT: V 203 MET cc_start: 0.8930 (mtm) cc_final: 0.8328 (mpp) REVERT: V 206 ILE cc_start: 0.9268 (mp) cc_final: 0.8996 (mm) REVERT: V 210 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: W 208 ILE cc_start: -0.3483 (OUTLIER) cc_final: -0.3851 (pp) REVERT: Z 91 PHE cc_start: 0.9641 (m-80) cc_final: 0.9094 (m-80) REVERT: Z 118 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8756 (mm-30) REVERT: a 162 LEU cc_start: 0.7905 (pt) cc_final: 0.7651 (pt) REVERT: b 73 HIS cc_start: 0.6587 (t70) cc_final: 0.6104 (t-90) REVERT: b 101 VAL cc_start: 0.7737 (t) cc_final: 0.7471 (t) REVERT: c 94 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8817 (tm-30) REVERT: d 115 GLN cc_start: 0.8603 (mt0) cc_final: 0.8131 (mm-40) REVERT: d 168 GLU cc_start: 0.9251 (pm20) cc_final: 0.8973 (pp20) REVERT: e 160 ILE cc_start: 0.9390 (pt) cc_final: 0.8737 (mm) REVERT: e 176 TYR cc_start: 0.7024 (m-80) cc_final: 0.6760 (m-80) REVERT: e 189 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7874 (tp) REVERT: e 202 SER cc_start: 0.9319 (m) cc_final: 0.9023 (p) REVERT: e 246 GLU cc_start: 0.7764 (tp30) cc_final: 0.7525 (tp30) REVERT: f 363 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7868 (tp) REVERT: h 27 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9264 (mp0) REVERT: h 30 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8848 (tp30) REVERT: i 98 ARG cc_start: 0.6720 (tpp80) cc_final: 0.6310 (tpt170) REVERT: j 833 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.4824 (m-80) REVERT: l 37 TYR cc_start: 0.8452 (p90) cc_final: 0.8123 (p90) REVERT: m 103 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.7949 (mp) REVERT: o 27 GLN cc_start: 0.8946 (tt0) cc_final: 0.8738 (tp-100) outliers start: 294 outliers final: 216 residues processed: 1022 average time/residue: 1.0830 time to fit residues: 1937.3279 Evaluate side-chains 986 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 752 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 299 SER Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 405 MET Chi-restraints excluded: chain z residue 409 PHE Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 106 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 264 HIS Chi-restraints excluded: chain H residue 290 MET Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain I residue 208 ASN Chi-restraints excluded: chain I residue 224 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 362 ASP Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 219 TYR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 81 TYR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 190 ASN Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 150 LYS Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 182 THR Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 220 ASP Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 249 ILE Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 83 ARG Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 228 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 347 LEU Chi-restraints excluded: chain f residue 355 THR Chi-restraints excluded: chain f residue 363 LEU Chi-restraints excluded: chain f residue 391 ARG Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 818 LYS Chi-restraints excluded: chain j residue 825 TYR Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 844 THR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain m residue 126 LYS Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 39 CYS Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 39 HIS Chi-restraints excluded: chain q residue 55 LYS Chi-restraints excluded: chain q residue 60 ARG Chi-restraints excluded: chain q residue 61 ARG 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: 0.0970 chunk 397 optimal weight: 0.4980 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: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** 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 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** ** D 305 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** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS L 19 GLN ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 194 ASN ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 HIS e 250 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 22 GLN ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 1.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.866 139014 Z= 0.636 Angle : 0.991 54.995 204868 Z= 0.491 Chirality : 0.052 1.964 25744 Planarity : 0.006 0.089 12919 Dihedral : 24.737 179.600 62128 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 34.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.76 % Favored : 86.06 % Rotamer: Outliers : 5.22 % Allowed : 29.57 % Favored : 65.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.57 % 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: -2.77 (0.10), residues: 6650 helix: -0.41 (0.11), residues: 2022 sheet: -1.69 (0.18), residues: 767 loop : -2.81 (0.09), residues: 3861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 120 HIS 0.039 0.002 HIS q 39 PHE 0.047 0.003 PHE N 21 TYR 0.057 0.003 TYR N 6 ARG 0.031 0.001 ARG N 24 *********************** 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 1077 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 789 time to evaluate : 6.511 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: z 369 MET cc_start: 0.8718 (ppp) cc_final: 0.8134 (pmm) REVERT: z 405 MET cc_start: 0.2592 (OUTLIER) cc_final: 0.2193 (mpp) REVERT: C 274 TYR cc_start: 0.5492 (t80) cc_final: 0.5263 (t80) REVERT: E 398 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6361 (pp) REVERT: F 295 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7658 (t80) REVERT: F 326 PHE cc_start: 0.7872 (m-10) cc_final: 0.7235 (m-10) REVERT: F 444 GLU cc_start: 0.9087 (mp0) cc_final: 0.8845 (mp0) REVERT: G 244 TYR cc_start: 0.9196 (m-80) cc_final: 0.8509 (m-80) REVERT: G 324 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8949 (mm) REVERT: G 334 CYS cc_start: 0.9152 (m) cc_final: 0.8923 (p) REVERT: G 391 ASP cc_start: 0.9305 (m-30) cc_final: 0.8921 (p0) REVERT: G 413 ARG cc_start: 0.9369 (ttt180) cc_final: 0.8913 (tpt90) REVERT: I 213 ASP cc_start: 0.9092 (m-30) cc_final: 0.8564 (t0) REVERT: I 251 GLU cc_start: 0.8992 (tp30) cc_final: 0.8651 (mm-30) REVERT: I 270 PHE cc_start: 0.9173 (p90) cc_final: 0.8832 (p90) REVERT: I 298 GLN cc_start: 0.7648 (mm-40) cc_final: 0.6913 (tp40) REVERT: I 401 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: J 219 TYR cc_start: 0.3418 (OUTLIER) cc_final: 0.2777 (t80) REVERT: L 10 LEU cc_start: 0.4762 (OUTLIER) cc_final: 0.4289 (mt) REVERT: M 165 GLU cc_start: 0.3335 (OUTLIER) cc_final: 0.2997 (pt0) REVERT: M 209 LEU cc_start: 0.6828 (pt) cc_final: 0.6596 (pt) REVERT: N 17 ASP cc_start: 0.0490 (OUTLIER) cc_final: 0.0153 (m-30) REVERT: N 29 GLU cc_start: 0.3330 (OUTLIER) cc_final: 0.2589 (mm-30) REVERT: N 116 LEU cc_start: 0.1162 (OUTLIER) cc_final: 0.0819 (mm) REVERT: N 148 TYR cc_start: 0.1639 (OUTLIER) cc_final: 0.0965 (m-80) REVERT: N 170 LYS cc_start: 0.0202 (OUTLIER) cc_final: -0.1676 (mmtt) REVERT: O 106 GLU cc_start: 0.6872 (mp0) cc_final: 0.6562 (mp0) REVERT: P 37 ASN cc_start: 0.9358 (t0) cc_final: 0.8328 (m110) REVERT: P 79 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7868 (t) REVERT: P 136 ILE cc_start: 0.8608 (pt) cc_final: 0.8290 (mp) REVERT: R 140 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8121 (mtt180) REVERT: R 261 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9028 (mm-30) REVERT: S 90 MET cc_start: 0.8632 (mtp) cc_final: 0.8157 (ttm) REVERT: T 98 HIS cc_start: 0.5549 (OUTLIER) cc_final: 0.5237 (t-170) REVERT: T 151 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7233 (mm) REVERT: V 161 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8620 (mtm-85) REVERT: V 188 MET cc_start: 0.9230 (mmp) cc_final: 0.8511 (mtm) REVERT: V 193 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8938 (ptmm) REVERT: V 203 MET cc_start: 0.8912 (mtm) cc_final: 0.8343 (mpp) REVERT: V 206 ILE cc_start: 0.9292 (mp) cc_final: 0.9061 (mm) REVERT: W 170 ASP cc_start: 0.4482 (p0) cc_final: 0.4092 (p0) REVERT: W 208 ILE cc_start: -0.3160 (OUTLIER) cc_final: -0.3627 (pp) REVERT: Z 91 PHE cc_start: 0.9640 (m-80) cc_final: 0.9109 (m-80) REVERT: Z 118 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8810 (mm-30) REVERT: b 73 HIS cc_start: 0.6830 (t70) cc_final: 0.6435 (t-90) REVERT: d 100 LEU cc_start: 0.8883 (tp) cc_final: 0.8549 (pp) REVERT: d 152 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8634 (pm20) REVERT: e 160 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8694 (mm) REVERT: e 176 TYR cc_start: 0.7282 (m-80) cc_final: 0.6805 (m-80) REVERT: e 189 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8116 (tp) REVERT: e 202 SER cc_start: 0.9312 (m) cc_final: 0.9023 (p) REVERT: h 30 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8756 (tp30) REVERT: i 98 ARG cc_start: 0.6671 (tpp80) cc_final: 0.6269 (tpt170) REVERT: j 833 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5034 (m-80) REVERT: l 30 ARG cc_start: 0.6629 (tpp80) cc_final: 0.6120 (tpp80) REVERT: m 103 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7975 (mp) outliers start: 288 outliers final: 218 residues processed: 978 average time/residue: 1.1673 time to fit residues: 2020.5801 Evaluate side-chains 971 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 731 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 400 VAL Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 405 MET Chi-restraints excluded: chain z residue 409 PHE Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 264 HIS Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain I residue 208 ASN Chi-restraints excluded: chain I residue 224 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 362 ASP Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 219 TYR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 275 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 190 ASN Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 182 THR Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 220 ASP Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain X residue 253 ILE Chi-restraints excluded: chain Y residue 83 ASP Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 83 ARG Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 205 ILE Chi-restraints excluded: chain a residue 228 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 71 LYS Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 101 HIS Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 189 ILE Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 250 ASN Chi-restraints excluded: chain e residue 270 VAL Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 347 LEU Chi-restraints excluded: chain f residue 355 THR Chi-restraints excluded: chain f residue 391 ARG Chi-restraints excluded: chain f residue 402 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 818 LYS Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 TRP Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 39 CYS Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 39 HIS Chi-restraints excluded: chain q residue 55 LYS Chi-restraints excluded: chain q residue 61 ARG 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: 5.9990 chunk 965 optimal weight: 20.0000 chunk 589 optimal weight: 5.9990 chunk 458 optimal weight: 5.9990 chunk 671 optimal weight: 20.0000 chunk 1013 optimal weight: 10.0000 chunk 932 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 623 optimal weight: 0.0060 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 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** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 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 156 HIS ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 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 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 GLN ** 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN Z 78 HIS a 106 HIS ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 ASN e 250 ASN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 834 ASN l 33 ASN ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 32 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 1.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.863 139014 Z= 0.636 Angle : 0.989 55.185 204868 Z= 0.489 Chirality : 0.049 1.886 25744 Planarity : 0.006 0.070 12919 Dihedral : 24.697 179.536 62128 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 33.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.96 % Favored : 86.90 % Rotamer: Outliers : 4.74 % Allowed : 30.46 % Favored : 64.80 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.73 (0.10), residues: 6650 helix: -0.41 (0.11), residues: 2007 sheet: -1.57 (0.18), residues: 778 loop : -2.78 (0.09), residues: 3865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 262 HIS 0.048 0.002 HIS d 101 PHE 0.043 0.002 PHE N 21 TYR 0.140 0.003 TYR N 6 ARG 0.029 0.001 ARG N 41 ********************** 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 1049 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 787 time to evaluate : 6.233 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: z 300 LYS cc_start: -0.4385 (OUTLIER) cc_final: -0.5542 (tttt) REVERT: z 369 MET cc_start: 0.8675 (ppp) cc_final: 0.8139 (pmm) REVERT: z 405 MET cc_start: 0.2383 (OUTLIER) cc_final: 0.2020 (mpp) REVERT: F 295 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7897 (t80) REVERT: F 326 PHE cc_start: 0.7783 (m-10) cc_final: 0.7225 (m-10) REVERT: F 444 GLU cc_start: 0.9123 (mp0) cc_final: 0.8888 (mp0) REVERT: G 244 TYR cc_start: 0.9251 (m-80) cc_final: 0.8547 (m-80) REVERT: G 324 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (mm) REVERT: G 334 CYS cc_start: 0.9132 (m) cc_final: 0.8918 (p) REVERT: G 413 ARG cc_start: 0.9440 (ttt180) cc_final: 0.8998 (tpt90) REVERT: I 213 ASP cc_start: 0.9160 (m-30) cc_final: 0.8679 (t0) REVERT: I 224 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8091 (mptt) REVERT: I 270 PHE cc_start: 0.9076 (p90) cc_final: 0.8872 (p90) REVERT: I 401 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: L 10 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.3845 (mt) REVERT: M 270 MET cc_start: 0.5217 (mmm) cc_final: 0.4540 (tpt) REVERT: N 17 ASP cc_start: 0.0658 (OUTLIER) cc_final: 0.0328 (m-30) REVERT: N 29 GLU cc_start: 0.3176 (OUTLIER) cc_final: 0.2474 (mm-30) REVERT: N 116 LEU cc_start: 0.1037 (OUTLIER) cc_final: 0.0771 (mm) REVERT: N 148 TYR cc_start: 0.1902 (OUTLIER) cc_final: 0.1255 (m-80) REVERT: N 170 LYS cc_start: 0.0438 (OUTLIER) cc_final: -0.1650 (mmtt) REVERT: O 27 LEU cc_start: 0.7689 (mm) cc_final: 0.7397 (mm) REVERT: O 106 GLU cc_start: 0.6793 (mp0) cc_final: 0.6485 (mp0) REVERT: P 37 ASN cc_start: 0.9405 (t0) cc_final: 0.8368 (m110) REVERT: P 113 TYR cc_start: 0.9192 (p90) cc_final: 0.8906 (p90) REVERT: P 136 ILE cc_start: 0.8487 (pt) cc_final: 0.8186 (mp) REVERT: R 140 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8110 (mtt180) REVERT: R 261 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9001 (mm-30) REVERT: S 90 MET cc_start: 0.8602 (mtp) cc_final: 0.8142 (ttm) REVERT: T 98 HIS cc_start: 0.5480 (OUTLIER) cc_final: 0.5243 (t-170) REVERT: T 151 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7188 (mm) REVERT: V 161 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8562 (mtm-85) REVERT: V 188 MET cc_start: 0.9236 (mmp) cc_final: 0.8438 (mtm) REVERT: V 193 LYS cc_start: 0.9358 (mtpt) cc_final: 0.8948 (ptmm) REVERT: V 203 MET cc_start: 0.8881 (mtm) cc_final: 0.8320 (mpp) REVERT: V 206 ILE cc_start: 0.9301 (mp) cc_final: 0.9056 (mm) REVERT: W 170 ASP cc_start: 0.4447 (p0) cc_final: 0.4148 (p0) REVERT: W 208 ILE cc_start: -0.2730 (OUTLIER) cc_final: -0.3280 (pp) REVERT: Z 91 PHE cc_start: 0.9640 (m-80) cc_final: 0.9136 (m-80) REVERT: Z 118 GLU cc_start: 0.9509 (mt-10) cc_final: 0.8938 (mm-30) REVERT: d 115 GLN cc_start: 0.8912 (mt0) cc_final: 0.8458 (mm-40) REVERT: e 160 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8702 (mm) REVERT: e 202 SER cc_start: 0.9342 (m) cc_final: 0.9043 (p) REVERT: h 12 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8535 (mtmm) REVERT: h 30 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8858 (tp30) REVERT: i 98 ARG cc_start: 0.6498 (tpp80) cc_final: 0.6105 (tpt170) REVERT: j 833 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5085 (m-80) REVERT: m 103 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8002 (mp) REVERT: o 35 LEU cc_start: 0.9048 (tp) cc_final: 0.8718 (tp) outliers start: 262 outliers final: 212 residues processed: 965 average time/residue: 1.0658 time to fit residues: 1814.1810 Evaluate side-chains 963 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 732 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 229 LEU Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 300 LYS Chi-restraints excluded: chain z residue 367 VAL Chi-restraints excluded: chain z residue 399 LEU Chi-restraints excluded: chain z residue 401 VAL Chi-restraints excluded: chain z residue 405 MET Chi-restraints excluded: chain z residue 410 ARG Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 445 PHE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 264 HIS Chi-restraints excluded: chain H residue 292 TYR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 208 ASN Chi-restraints excluded: chain I residue 224 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 234 CYS Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 330 LYS Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 362 ASP Chi-restraints excluded: chain I residue 381 PHE Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 401 TYR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain J residue 219 TYR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 SER Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 112 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain N residue 184 LYS Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 170 ASN Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 270 ASN Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 65 ASN Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 45 ASN Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 181 GLU Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 210 GLN Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 190 ASN Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain X residue 150 LYS Chi-restraints excluded: chain X residue 182 THR Chi-restraints excluded: chain X residue 195 ILE Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 220 ASP Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 83 ASP Chi-restraints excluded: chain Y residue 98 ASN Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 83 ARG Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain a residue 97 SER Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 158 LYS Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 229 ILE Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain d residue 164 THR Chi-restraints excluded: chain e residue 160 ILE Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 201 ILE Chi-restraints excluded: chain e residue 250 ASN Chi-restraints excluded: chain e residue 270 VAL Chi-restraints excluded: chain f residue 339 ARG Chi-restraints excluded: chain f residue 340 VAL Chi-restraints excluded: chain f residue 347 LEU Chi-restraints excluded: chain f residue 355 THR Chi-restraints excluded: chain f residue 391 ARG Chi-restraints excluded: chain f residue 402 THR Chi-restraints excluded: chain f residue 415 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 ASN Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain j residue 801 SER Chi-restraints excluded: chain j residue 805 CYS Chi-restraints excluded: chain j residue 831 ARG Chi-restraints excluded: chain j residue 833 TYR Chi-restraints excluded: chain j residue 834 ASN Chi-restraints excluded: chain j residue 857 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 36 ARG Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 39 CYS Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 39 HIS Chi-restraints excluded: chain q residue 55 LYS Chi-restraints excluded: chain q residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 494 optimal weight: 4.9990 chunk 640 optimal weight: 7.9990 chunk 859 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 743 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 808 optimal weight: 9.9990 chunk 338 optimal weight: 0.9990 chunk 829 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 181 GLN ** 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** ** M 254 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 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 149 GLN ** 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 834 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** o 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.045936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.034568 restraints weight = 1127961.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.035833 restraints weight = 419016.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036582 restraints weight = 228679.845| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 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 = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 1.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.905 139014 Z= 0.645 Angle : 1.017 59.184 204868 Z= 0.515 Chirality : 0.050 1.888 25744 Planarity : 0.006 0.096 12919 Dihedral : 24.698 179.496 62127 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 34.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.25 % Favored : 86.63 % Rotamer: Outliers : 4.78 % Allowed : 30.57 % Favored : 64.65 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.73 (0.10), residues: 6650 helix: -0.40 (0.11), residues: 2007 sheet: -1.55 (0.18), residues: 778 loop : -2.79 (0.09), residues: 3865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 262 HIS 0.082 0.002 HIS O 55 PHE 0.051 0.003 PHE L 14 TYR 0.110 0.003 TYR N 6 ARG 0.107 0.001 ARG N 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33603.71 seconds wall clock time: 589 minutes 55.88 seconds (35395.88 seconds total)