Starting phenix.real_space_refine on Sun May 25 10:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.map" model { file = "/net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q91_18267/05_2025/8q91_18267.cif" } resolution = 3.1 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= -0.000 sd= 0.016 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 106 5.49 5 S 93 5.16 5 C 16557 2.51 5 N 4707 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26706 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 887 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 13247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1627, 13247 Classifications: {'peptide': 1627} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 3, 'PTRANS': 90, 'TRANS': 1533} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "5" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2192 Classifications: {'RNA': 104} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Chain: "C" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6629 Classifications: {'peptide': 847} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 49, 'TRANS': 797} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "m" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "n" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 364 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "i" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 401 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "j" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 487 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 165 Chain: "k" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 414 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "h" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 360 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 125 Chain: "l" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 381 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.39, per 1000 atoms: 0.65 Number of scatterers: 26706 At special positions: 0 Unit cell: (123.298, 165.094, 219.429, 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 93 16.00 P 106 15.00 O 5243 8.00 N 4707 7.00 C 16557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.7 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 43.7% alpha, 17.0% beta 34 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 11.71 Creating SS restraints... Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.895A pdb=" N VAL F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 92 through 99 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.577A pdb=" N ASN F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 196 through 212 Processing helix chain 'F' and resid 216 through 220 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.345A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.802A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.737A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 removed outlier: 3.623A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.567A pdb=" N LYS A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 566 removed outlier: 3.780A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 590 through 596 removed outlier: 3.671A pdb=" N ARG A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A 596 " --> pdb=" O ARG A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.137A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 656 removed outlier: 3.832A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 681 through 696 Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 850 removed outlier: 3.894A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.979A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1135 through 1139 Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.505A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1274 through 1281 removed outlier: 4.034A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1341 removed outlier: 3.508A pdb=" N LEU A1340 " --> pdb=" O GLN A1337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.583A pdb=" N ARG A1370 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.520A pdb=" N TRP A1412 " --> pdb=" O GLU A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 3.704A pdb=" N GLN A1424 " --> pdb=" O THR A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1444 removed outlier: 4.022A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 4.037A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1493 Processing helix chain 'A' and resid 1531 through 1538 Processing helix chain 'A' and resid 1539 through 1542 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1601 through 1605 Processing helix chain 'A' and resid 1617 through 1621 Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.910A pdb=" N THR A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1737 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'E' and resid 96 through 114 Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 138 through 150 removed outlier: 5.207A pdb=" N ASP E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 145 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.622A pdb=" N GLU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.854A pdb=" N PHE C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.752A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 265 removed outlier: 3.831A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 312 through 315 Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.622A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.766A pdb=" N THR C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 3.577A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.013A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 468 removed outlier: 3.686A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.671A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.517A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 755 through 777 removed outlier: 3.699A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 823 removed outlier: 3.986A pdb=" N THR C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 852 removed outlier: 3.725A pdb=" N ARG C 852 " --> pdb=" O THR C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 881 removed outlier: 4.119A pdb=" N PHE C 881 " --> pdb=" O ILE C 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 878 through 881' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.698A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 14 removed outlier: 3.517A pdb=" N LEU m 14 " --> pdb=" O PHE m 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 13 Processing helix chain 'n' and resid 64 through 67 Processing helix chain 'i' and resid 3 through 9 Processing helix chain 'i' and resid 75 through 80 Processing helix chain 'j' and resid 18 through 23 Processing helix chain 'j' and resid 29 through 39 removed outlier: 3.551A pdb=" N THR j 33 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER j 35 " --> pdb=" O VAL j 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 13 Processing helix chain 'k' and resid 74 through 84 Proline residue: k 81 - end of helix Processing helix chain 'h' and resid 7 through 11 Processing helix chain 'l' and resid 16 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 910 removed outlier: 3.722A pdb=" N LEU A 901 " --> pdb=" O HIS A 904 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 5.341A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A1095 " --> pdb=" O SER A 979 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 3.581A pdb=" N ALA A1226 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1342 through 1346 Processing sheet with id=AA9, first strand: chain 'A' and resid 1553 through 1554 removed outlier: 3.863A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1608 through 1611 removed outlier: 8.618A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N TRP A1637 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER A1654 " --> pdb=" O TRP A1637 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A1639 " --> pdb=" O MET A1652 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET A1652 " --> pdb=" O VAL A1639 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 191 removed outlier: 9.012A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 523 through 526 removed outlier: 7.227A pdb=" N CYS C 476 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 497 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AB6, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.777A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.777A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.402A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 783 through 784 removed outlier: 7.162A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.147A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 23 removed outlier: 4.829A pdb=" N MET m 27 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU m 28 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU m 49 " --> pdb=" O GLU m 28 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS m 30 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR m 47 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR m 32 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA m 45 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN m 43 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN m 43 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL m 62 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA m 45 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY m 60 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N THR m 47 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS m 58 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLU m 49 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU m 61 " --> pdb=" O ARG j 111 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG j 111 " --> pdb=" O GLU m 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS j 51 " --> pdb=" O GLU j 72 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU j 72 " --> pdb=" O LYS j 51 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU j 53 " --> pdb=" O VAL j 70 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL j 70 " --> pdb=" O LEU j 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG j 55 " --> pdb=" O GLU j 68 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL j 66 " --> pdb=" O LYS j 57 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU j 67 " --> pdb=" O MET j 99 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER j 97 " --> pdb=" O ASN j 69 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS j 71 " --> pdb=" O TYR j 95 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR j 95 " --> pdb=" O LYS j 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET j 73 " --> pdb=" O ASP j 93 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP j 93 " --> pdb=" O MET j 73 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR j 75 " --> pdb=" O ASN j 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN j 91 " --> pdb=" O THR j 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS j 98 " --> pdb=" O LEU i 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR i 16 " --> pdb=" O ILE i 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU i 13 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR i 28 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA i 42 " --> pdb=" O THR i 28 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR i 30 " --> pdb=" O LEU i 40 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU i 40 " --> pdb=" O THR i 30 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL i 32 " --> pdb=" O THR i 38 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR i 38 " --> pdb=" O VAL i 32 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU i 56 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS i 44 " --> pdb=" O GLN i 54 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN i 54 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 14.070A pdb=" N LEU i 55 " --> pdb=" O GLY h 84 " (cutoff:3.500A) removed outlier: 12.299A pdb=" N GLY h 84 " --> pdb=" O LEU i 55 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR i 57 " --> pdb=" O VAL h 82 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL h 82 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG h 16 " --> pdb=" O GLU h 83 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR h 30 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP h 44 " --> pdb=" O THR h 30 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS h 32 " --> pdb=" O LEU h 42 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU h 42 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE h 34 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU h 40 " --> pdb=" O PHE h 34 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY h 68 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP h 46 " --> pdb=" O VAL h 66 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL h 66 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE h 48 " --> pdb=" O LYS h 64 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS h 64 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU h 69 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU k 21 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU k 71 " --> pdb=" O THR k 19 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR k 19 " --> pdb=" O LEU k 71 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU k 73 " --> pdb=" O ILE k 17 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE k 17 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL k 27 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL k 48 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG k 29 " --> pdb=" O ILE k 46 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE k 46 " --> pdb=" O ARG k 29 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN k 42 " --> pdb=" O TYR k 62 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR k 62 " --> pdb=" O GLN k 42 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER k 44 " --> pdb=" O GLN k 60 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN k 60 " --> pdb=" O SER k 44 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN k 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA n 72 " --> pdb=" O GLN k 60 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS n 20 " --> pdb=" O MET n 69 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN n 28 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS n 45 " --> pdb=" O GLN n 28 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS l 46 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP l 60 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE l 48 " --> pdb=" O LEU l 58 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL l 57 " --> pdb=" O MET l 78 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET l 78 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP l 59 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS m 22 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE m 72 " --> pdb=" O MET m 20 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET m 20 " --> pdb=" O ILE m 72 " (cutoff:3.500A) 1201 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 14.23 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8493 1.34 - 1.46: 6507 1.46 - 1.58: 12116 1.58 - 1.70: 209 1.70 - 1.83: 152 Bond restraints: 27477 Sorted by residual: bond pdb=" N CYS C 144 " pdb=" CA CYS C 144 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.20e-02 6.94e+03 8.72e+00 bond pdb=" N LEU C 149 " pdb=" CA LEU C 149 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.35e-02 5.49e+03 8.65e+00 bond pdb=" N ASN m 41 " pdb=" CA ASN m 41 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL C 146 " pdb=" CA VAL C 146 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" N TYR m 39 " pdb=" CA TYR m 39 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.89e+00 ... (remaining 27472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 37407 2.70 - 5.40: 418 5.40 - 8.10: 48 8.10 - 10.79: 16 10.79 - 13.49: 5 Bond angle restraints: 37894 Sorted by residual: angle pdb=" C VAL l 15 " pdb=" N GLN l 16 " pdb=" CA GLN l 16 " ideal model delta sigma weight residual 121.76 135.25 -13.49 1.74e+00 3.30e-01 6.01e+01 angle pdb=" N CYS C 144 " pdb=" CA CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sigma weight residual 109.94 120.47 -10.53 1.49e+00 4.50e-01 4.99e+01 angle pdb=" N LEU h 10 " pdb=" CA LEU h 10 " pdb=" C LEU h 10 " ideal model delta sigma weight residual 112.54 105.44 7.10 1.22e+00 6.72e-01 3.38e+01 angle pdb=" CA ILE A 867 " pdb=" CB ILE A 867 " pdb=" CG1 ILE A 867 " ideal model delta sigma weight residual 110.40 119.73 -9.33 1.70e+00 3.46e-01 3.01e+01 angle pdb=" C CYS C 144 " pdb=" CA CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sigma weight residual 110.81 102.51 8.30 1.60e+00 3.91e-01 2.69e+01 ... (remaining 37889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 15840 35.12 - 70.24: 636 70.24 - 105.36: 57 105.36 - 140.48: 3 140.48 - 175.59: 8 Dihedral angle restraints: 16544 sinusoidal: 6871 harmonic: 9673 Sorted by residual: dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual -128.00 46.88 -174.88 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 65.38 166.62 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 232.00 71.13 160.87 1 1.70e+01 3.46e-03 6.46e+01 ... (remaining 16541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3952 0.075 - 0.150: 421 0.150 - 0.225: 19 0.225 - 0.300: 2 0.300 - 0.375: 1 Chirality restraints: 4395 Sorted by residual: chirality pdb=" CA THR C 143 " pdb=" N THR C 143 " pdb=" C THR C 143 " pdb=" CB THR C 143 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA MET j 99 " pdb=" N MET j 99 " pdb=" C MET j 99 " pdb=" CB MET j 99 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' GTP C1001 " pdb=" C2' GTP C1001 " pdb=" C4' GTP C1001 " pdb=" O3' GTP C1001 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4392 not shown) Planarity restraints: 4549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 5 57 " -0.055 2.00e-02 2.50e+03 2.45e-02 1.80e+01 pdb=" N9 G 5 57 " 0.060 2.00e-02 2.50e+03 pdb=" C8 G 5 57 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 5 57 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 5 57 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 5 57 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G 5 57 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G 5 57 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 5 57 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 5 57 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G 5 57 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1342 " -0.030 2.00e-02 2.50e+03 2.67e-02 1.79e+01 pdb=" CG TRP A1342 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A1342 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A1342 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A1342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1342 " 0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A1342 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1342 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1342 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1482 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" CD GLU A1482 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU A1482 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A1482 " -0.021 2.00e-02 2.50e+03 ... (remaining 4546 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 325 2.62 - 3.19: 23539 3.19 - 3.76: 43132 3.76 - 4.33: 58360 4.33 - 4.90: 93515 Nonbonded interactions: 218871 Sorted by model distance: nonbonded pdb=" O MET A1622 " pdb=" OH TYR A1687 " model vdw 2.047 3.040 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.093 3.040 nonbonded pdb=" OG SER A1625 " pdb=" OD2 ASP A1663 " model vdw 2.136 3.040 nonbonded pdb=" O2' G 5 57 " pdb=" O5' U 5 58 " model vdw 2.161 3.040 nonbonded pdb=" O LEU A1536 " pdb=" OG SER A1539 " model vdw 2.179 3.040 ... (remaining 218866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 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: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 75.410 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.004 0.066 27478 Z= 0.184 Angle : 0.730 13.492 37896 Z= 0.393 Chirality : 0.045 0.375 4395 Planarity : 0.005 0.104 4549 Dihedral : 18.346 175.595 10265 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.18 % Allowed : 21.88 % Favored : 75.94 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3267 helix: 1.19 (0.15), residues: 1231 sheet: -0.27 (0.23), residues: 470 loop : -0.74 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1342 HIS 0.014 0.001 HIS A1024 PHE 0.023 0.002 PHE C 717 TYR 0.021 0.002 TYR A 783 ARG 0.014 0.001 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.17231 ( 1271) hydrogen bonds : angle 6.81498 ( 3514) SS BOND : bond 0.02878 ( 1) SS BOND : angle 7.25479 ( 2) covalent geometry : bond 0.00371 (27477) covalent geometry : angle 0.72820 (37894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 228 average time/residue: 0.3387 time to fit residues: 128.9904 Evaluate side-chains 221 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 171 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 101 optimal weight: 0.0070 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1610 GLN C 139 HIS C 335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.110681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074133 restraints weight = 76259.276| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.55 r_work: 0.3027 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27478 Z= 0.152 Angle : 0.588 10.179 37896 Z= 0.304 Chirality : 0.043 0.207 4395 Planarity : 0.004 0.052 4549 Dihedral : 16.283 175.011 5227 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 18.81 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3267 helix: 1.53 (0.15), residues: 1270 sheet: -0.29 (0.23), residues: 500 loop : -0.50 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1342 HIS 0.005 0.001 HIS A1712 PHE 0.019 0.001 PHE A1597 TYR 0.017 0.001 TYR A1008 ARG 0.006 0.000 ARG A1090 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1271) hydrogen bonds : angle 5.04034 ( 3514) SS BOND : bond 0.02206 ( 1) SS BOND : angle 8.91014 ( 2) covalent geometry : bond 0.00339 (27477) covalent geometry : angle 0.58431 (37894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8639 (m-10) REVERT: A 1622 MET cc_start: 0.8051 (mpt) cc_final: 0.7799 (mpt) REVERT: A 1709 TYR cc_start: 0.7082 (m-80) cc_final: 0.6746 (m-80) REVERT: D 275 GLU cc_start: 0.8312 (mp0) cc_final: 0.8053 (tt0) REVERT: C 147 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7975 (p0) REVERT: C 807 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7909 (tp40) outliers start: 69 outliers final: 33 residues processed: 253 average time/residue: 0.3661 time to fit residues: 150.5156 Evaluate side-chains 217 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 254 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 294 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 188 optimal weight: 40.0000 chunk 303 optimal weight: 0.0970 chunk 184 optimal weight: 30.0000 chunk 156 optimal weight: 3.9990 chunk 301 optimal weight: 30.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 834 HIS A1023 ASN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.107677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.070169 restraints weight = 76641.385| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.47 r_work: 0.2948 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 27478 Z= 0.328 Angle : 0.675 11.108 37896 Z= 0.347 Chirality : 0.047 0.257 4395 Planarity : 0.005 0.057 4549 Dihedral : 16.222 178.369 5189 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 4.22 % Allowed : 18.23 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3267 helix: 1.39 (0.15), residues: 1272 sheet: -0.27 (0.24), residues: 481 loop : -0.61 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 637 HIS 0.007 0.002 HIS C 928 PHE 0.027 0.002 PHE A1099 TYR 0.019 0.002 TYR A 431 ARG 0.006 0.001 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 1271) hydrogen bonds : angle 4.94839 ( 3514) SS BOND : bond 0.03248 ( 1) SS BOND : angle 10.56337 ( 2) covalent geometry : bond 0.00772 (27477) covalent geometry : angle 0.67020 (37894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 180 time to evaluate : 2.831 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8804 (m-10) REVERT: A 1067 MET cc_start: 0.8710 (tpt) cc_final: 0.8319 (ppp) REVERT: A 1123 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8566 (mp0) REVERT: A 1307 MET cc_start: 0.7653 (pmm) cc_final: 0.7142 (pmm) REVERT: D 275 GLU cc_start: 0.8289 (mp0) cc_final: 0.8029 (tt0) REVERT: C 793 ASP cc_start: 0.7961 (t0) cc_final: 0.7195 (p0) REVERT: C 807 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: C 822 MET cc_start: 0.8576 (mmt) cc_final: 0.8251 (mmm) outliers start: 95 outliers final: 53 residues processed: 257 average time/residue: 0.3444 time to fit residues: 147.8955 Evaluate side-chains 224 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 944 SER Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 3 optimal weight: 8.9990 chunk 213 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 287 optimal weight: 50.0000 chunk 171 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 275 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 77 optimal weight: 50.0000 chunk 302 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 ASN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.108277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071181 restraints weight = 77169.830| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.54 r_work: 0.2954 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27478 Z= 0.219 Angle : 0.590 10.503 37896 Z= 0.305 Chirality : 0.044 0.227 4395 Planarity : 0.004 0.056 4549 Dihedral : 16.133 179.568 5186 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 3.60 % Allowed : 18.50 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3267 helix: 1.59 (0.15), residues: 1267 sheet: -0.23 (0.24), residues: 481 loop : -0.55 (0.17), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 637 HIS 0.005 0.001 HIS A1712 PHE 0.021 0.001 PHE A1099 TYR 0.020 0.002 TYR F 107 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 1271) hydrogen bonds : angle 4.69100 ( 3514) SS BOND : bond 0.02864 ( 1) SS BOND : angle 9.76790 ( 2) covalent geometry : bond 0.00509 (27477) covalent geometry : angle 0.58587 (37894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 2.955 Fit side-chains revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: F 219 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: A 297 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8845 (p0) REVERT: A 474 ARG cc_start: 0.9452 (OUTLIER) cc_final: 0.9136 (mtt-85) REVERT: A 832 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: A 981 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8660 (m-10) REVERT: A 1067 MET cc_start: 0.8779 (tpt) cc_final: 0.8379 (ppp) REVERT: A 1123 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8542 (mp0) REVERT: A 1597 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7372 (t80) REVERT: D 275 GLU cc_start: 0.8323 (mp0) cc_final: 0.8043 (tt0) REVERT: C 793 ASP cc_start: 0.8054 (t0) cc_final: 0.7251 (p0) REVERT: C 807 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7862 (tp40) REVERT: C 822 MET cc_start: 0.8676 (mmt) cc_final: 0.8320 (mmm) outliers start: 81 outliers final: 52 residues processed: 244 average time/residue: 0.3563 time to fit residues: 144.3286 Evaluate side-chains 234 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 832 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 135 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 203 optimal weight: 0.0570 chunk 222 optimal weight: 0.9980 chunk 320 optimal weight: 40.0000 chunk 187 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.108954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071564 restraints weight = 76632.345| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.32 r_work: 0.2993 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27478 Z= 0.151 Angle : 0.554 9.585 37896 Z= 0.284 Chirality : 0.042 0.231 4395 Planarity : 0.004 0.055 4549 Dihedral : 16.015 177.638 5184 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 3.33 % Allowed : 19.08 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3267 helix: 1.74 (0.15), residues: 1270 sheet: -0.20 (0.24), residues: 487 loop : -0.45 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1342 HIS 0.004 0.001 HIS C 928 PHE 0.019 0.001 PHE A1099 TYR 0.018 0.001 TYR F 107 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1271) hydrogen bonds : angle 4.49170 ( 3514) SS BOND : bond 0.02602 ( 1) SS BOND : angle 8.88676 ( 2) covalent geometry : bond 0.00347 (27477) covalent geometry : angle 0.55032 (37894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7237 (ttm170) REVERT: F 198 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7514 (tpt-90) REVERT: F 219 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8302 (mm110) REVERT: A 297 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8977 (p0) REVERT: A 474 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9080 (mtt-85) REVERT: A 981 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: A 1067 MET cc_start: 0.8768 (tpt) cc_final: 0.8389 (ppp) REVERT: A 1123 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8517 (mp0) REVERT: D 245 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7670 (mtpt) REVERT: D 275 GLU cc_start: 0.8323 (mp0) cc_final: 0.8033 (tt0) REVERT: C 176 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: C 793 ASP cc_start: 0.7960 (t0) cc_final: 0.7239 (p0) REVERT: C 807 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7809 (tp40) outliers start: 75 outliers final: 48 residues processed: 239 average time/residue: 0.3587 time to fit residues: 143.9980 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 88 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 238 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1056 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1424 GLN ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** 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 = 0.4053 r_free = 0.4053 target = 0.108895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071316 restraints weight = 76718.064| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.48 r_work: 0.2992 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27478 Z= 0.152 Angle : 0.546 9.413 37896 Z= 0.279 Chirality : 0.042 0.302 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.912 175.653 5181 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.72 % Rotamer: Outliers : 3.38 % Allowed : 19.65 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3267 helix: 1.83 (0.15), residues: 1277 sheet: -0.21 (0.24), residues: 493 loop : -0.38 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1342 HIS 0.006 0.001 HIS A1024 PHE 0.017 0.001 PHE A1099 TYR 0.017 0.001 TYR F 107 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1271) hydrogen bonds : angle 4.35739 ( 3514) SS BOND : bond 0.02661 ( 1) SS BOND : angle 8.78733 ( 2) covalent geometry : bond 0.00352 (27477) covalent geometry : angle 0.54194 (37894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: F 198 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7579 (tpt-90) REVERT: F 219 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8339 (mm110) REVERT: A 297 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9061 (p0) REVERT: A 474 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9042 (mtt-85) REVERT: A 530 LEU cc_start: 0.8300 (tp) cc_final: 0.8075 (tp) REVERT: A 981 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8678 (m-10) REVERT: A 1067 MET cc_start: 0.8802 (tpt) cc_final: 0.8341 (ppp) REVERT: A 1123 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8451 (mp0) REVERT: D 245 LYS cc_start: 0.8297 (mptt) cc_final: 0.7678 (mtpt) REVERT: D 275 GLU cc_start: 0.8285 (mp0) cc_final: 0.7974 (tt0) REVERT: C 176 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: C 793 ASP cc_start: 0.7937 (t0) cc_final: 0.7395 (p0) REVERT: C 807 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7798 (tp40) outliers start: 76 outliers final: 52 residues processed: 242 average time/residue: 0.3391 time to fit residues: 137.7736 Evaluate side-chains 238 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 206 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.0270 chunk 225 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071498 restraints weight = 76730.126| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.65 r_work: 0.2968 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27478 Z= 0.169 Angle : 0.554 9.614 37896 Z= 0.284 Chirality : 0.043 0.264 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.870 175.308 5180 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 3.51 % Allowed : 19.56 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3267 helix: 1.88 (0.15), residues: 1277 sheet: -0.12 (0.24), residues: 503 loop : -0.37 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1342 HIS 0.005 0.001 HIS C 928 PHE 0.018 0.001 PHE A1099 TYR 0.014 0.001 TYR F 107 ARG 0.007 0.000 ARG A1354 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 1271) hydrogen bonds : angle 4.34407 ( 3514) SS BOND : bond 0.02766 ( 1) SS BOND : angle 8.94394 ( 2) covalent geometry : bond 0.00394 (27477) covalent geometry : angle 0.55038 (37894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 182 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7184 (ttm170) REVERT: F 219 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8411 (mm110) REVERT: A 86 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7914 (tpp80) REVERT: A 297 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.9007 (p0) REVERT: A 474 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.9068 (mtt-85) REVERT: A 530 LEU cc_start: 0.8270 (tp) cc_final: 0.8020 (tp) REVERT: A 981 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: A 1067 MET cc_start: 0.8605 (tpt) cc_final: 0.8176 (tmm) REVERT: A 1123 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8469 (mp0) REVERT: A 1282 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: A 1342 TRP cc_start: 0.6240 (p90) cc_final: 0.5795 (p-90) REVERT: D 245 LYS cc_start: 0.8312 (mptt) cc_final: 0.7691 (mtpt) REVERT: D 275 GLU cc_start: 0.8305 (mp0) cc_final: 0.8003 (tt0) REVERT: C 176 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 793 ASP cc_start: 0.8039 (t0) cc_final: 0.7551 (p0) REVERT: C 807 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7712 (tt0) outliers start: 79 outliers final: 58 residues processed: 247 average time/residue: 0.3544 time to fit residues: 147.1306 Evaluate side-chains 243 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1282 GLN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 166 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 310 optimal weight: 50.0000 chunk 214 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 287 optimal weight: 50.0000 chunk 279 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1024 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 HIS ** A1610 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.109476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072230 restraints weight = 76883.041| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.52 r_work: 0.3003 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27478 Z= 0.120 Angle : 0.536 10.295 37896 Z= 0.272 Chirality : 0.042 0.225 4395 Planarity : 0.004 0.053 4549 Dihedral : 15.798 176.905 5180 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.18 % Rotamer: Outliers : 2.80 % Allowed : 20.23 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3267 helix: 1.99 (0.15), residues: 1273 sheet: -0.03 (0.24), residues: 509 loop : -0.31 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1661 HIS 0.004 0.001 HIS C 928 PHE 0.017 0.001 PHE A1597 TYR 0.015 0.001 TYR A1695 ARG 0.006 0.000 ARG A1310 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1271) hydrogen bonds : angle 4.24675 ( 3514) SS BOND : bond 0.02397 ( 1) SS BOND : angle 8.08895 ( 2) covalent geometry : bond 0.00271 (27477) covalent geometry : angle 0.53249 (37894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7415 (ttm170) REVERT: F 118 SER cc_start: 0.8924 (t) cc_final: 0.8495 (m) REVERT: A 297 ASN cc_start: 0.9344 (OUTLIER) cc_final: 0.9083 (p0) REVERT: A 530 LEU cc_start: 0.8246 (tp) cc_final: 0.7989 (tp) REVERT: A 981 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: A 1123 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8465 (mp0) REVERT: A 1282 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7814 (mm-40) REVERT: D 245 LYS cc_start: 0.8287 (mptt) cc_final: 0.7671 (mtpt) REVERT: D 275 GLU cc_start: 0.8290 (mp0) cc_final: 0.7991 (tt0) REVERT: C 176 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: C 793 ASP cc_start: 0.8080 (t0) cc_final: 0.7566 (p0) REVERT: C 807 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7668 (tt0) outliers start: 63 outliers final: 45 residues processed: 236 average time/residue: 0.3544 time to fit residues: 139.9682 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1282 GLN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN A 357 ASN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.109074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071570 restraints weight = 77270.204| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.54 r_work: 0.2990 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27478 Z= 0.146 Angle : 0.556 11.058 37896 Z= 0.281 Chirality : 0.042 0.270 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.785 177.239 5180 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.67 % Allowed : 20.45 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3267 helix: 1.96 (0.15), residues: 1276 sheet: 0.01 (0.24), residues: 499 loop : -0.30 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1661 HIS 0.006 0.001 HIS A1024 PHE 0.018 0.001 PHE A1099 TYR 0.015 0.001 TYR C 167 ARG 0.007 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1271) hydrogen bonds : angle 4.24938 ( 3514) SS BOND : bond 0.02563 ( 1) SS BOND : angle 8.44822 ( 2) covalent geometry : bond 0.00340 (27477) covalent geometry : angle 0.55276 (37894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: F 169 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 297 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8936 (p0) REVERT: A 530 LEU cc_start: 0.8275 (tp) cc_final: 0.8019 (tp) REVERT: A 981 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: A 1107 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7918 (mmm160) REVERT: A 1123 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8463 (mp0) REVERT: A 1597 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7362 (t80) REVERT: D 245 LYS cc_start: 0.8297 (mptt) cc_final: 0.7696 (mtpt) REVERT: D 275 GLU cc_start: 0.8255 (mp0) cc_final: 0.7964 (tt0) REVERT: C 176 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: C 793 ASP cc_start: 0.8090 (t0) cc_final: 0.7603 (p0) REVERT: C 807 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: C 943 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9190 (mt) outliers start: 60 outliers final: 45 residues processed: 230 average time/residue: 0.3521 time to fit residues: 135.4556 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 137 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 47 optimal weight: 0.3980 chunk 331 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 303 optimal weight: 0.2980 chunk 321 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 282 optimal weight: 7.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1610 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.109023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072231 restraints weight = 77345.940| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.92 r_work: 0.2978 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27478 Z= 0.146 Angle : 0.552 9.985 37896 Z= 0.279 Chirality : 0.042 0.309 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.729 177.566 5180 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 2.45 % Allowed : 20.19 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3267 helix: 1.94 (0.15), residues: 1283 sheet: 0.06 (0.24), residues: 494 loop : -0.32 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1342 HIS 0.005 0.001 HIS A1024 PHE 0.018 0.001 PHE A1099 TYR 0.014 0.001 TYR C 167 ARG 0.010 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 1271) hydrogen bonds : angle 4.24300 ( 3514) SS BOND : bond 0.02578 ( 1) SS BOND : angle 8.50469 ( 2) covalent geometry : bond 0.00340 (27477) covalent geometry : angle 0.54859 (37894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7340 (ttm170) REVERT: F 169 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7183 (mt-10) REVERT: F 198 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7548 (tpt-90) REVERT: A 297 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8977 (p0) REVERT: A 530 LEU cc_start: 0.8190 (tp) cc_final: 0.7935 (tp) REVERT: A 981 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: A 1107 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7939 (mmm160) REVERT: A 1123 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8469 (mp0) REVERT: A 1597 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7363 (t80) REVERT: D 245 LYS cc_start: 0.8399 (mptt) cc_final: 0.7785 (mtpt) REVERT: D 275 GLU cc_start: 0.8271 (mp0) cc_final: 0.7940 (tt0) REVERT: C 176 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: C 793 ASP cc_start: 0.8124 (t0) cc_final: 0.7631 (p0) REVERT: C 807 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: C 943 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9205 (mt) REVERT: C 949 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7167 (tt) outliers start: 55 outliers final: 44 residues processed: 223 average time/residue: 0.3509 time to fit residues: 131.2885 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 167 optimal weight: 2.9990 chunk 324 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 303 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 331 optimal weight: 30.0000 chunk 312 optimal weight: 10.0000 chunk 323 optimal weight: 30.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS ** A1610 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.107851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069903 restraints weight = 77239.791| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.57 r_work: 0.2960 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 27478 Z= 0.212 Angle : 0.594 10.172 37896 Z= 0.301 Chirality : 0.044 0.295 4395 Planarity : 0.004 0.055 4549 Dihedral : 15.742 176.670 5179 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.76 % Allowed : 19.96 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3267 helix: 1.91 (0.15), residues: 1280 sheet: -0.01 (0.24), residues: 494 loop : -0.36 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1342 HIS 0.006 0.001 HIS C 928 PHE 0.022 0.002 PHE A1099 TYR 0.030 0.002 TYR A1494 ARG 0.010 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1271) hydrogen bonds : angle 4.36440 ( 3514) SS BOND : bond 0.03050 ( 1) SS BOND : angle 9.45915 ( 2) covalent geometry : bond 0.00494 (27477) covalent geometry : angle 0.58999 (37894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16070.81 seconds wall clock time: 278 minutes 44.98 seconds (16724.98 seconds total)