Starting phenix.real_space_refine on Sat Jul 4 01:30:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bde_44450/07_2026/9bde_44450.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 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 Ca 7 9.91 5 S 77 5.16 5 C 10789 2.51 5 N 2876 2.21 5 O 3467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17216 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1289 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 4 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 8453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8453 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 31, 'TRANS': 1089} Chain breaks: 10 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 4, 'ARG:plan': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'TYR:plan': 3, 'PHE:plan': 9, 'GLN:plan1': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 233 Chain: "L" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1244 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 4 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 153 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 4, 'ASP:plan': 4, 'TYR:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3396 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 24, 'TRANS': 441} Chain breaks: 6 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 859 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1898 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 152 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 11, 'ASN:plan1': 3, 'GLN:plan1': 6, 'GLU:plan': 5, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 0 Ad-hoc single atom residues: {' CA': 7} Chain breaks: 7 Time building chain proxies: 2.98, per 1000 atoms: 0.17 Number of scatterers: 17216 At special positions: 0 Unit cell: (185.92, 192.56, 207.5, 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) Ca 7 19.99 S 77 16.00 O 3467 8.00 N 2876 7.00 C 10789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 68 " - pdb=" SG CYS R 82 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 143 " distance=2.03 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS R 155 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS R 167 " - pdb=" SG CYS R 184 " distance=2.03 Simple disulfide: pdb=" SG CYS R 197 " - pdb=" SG CYS R 209 " distance=2.03 Simple disulfide: pdb=" SG CYS R 204 " - pdb=" SG CYS R 222 " distance=2.04 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 231 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 248 " distance=2.03 Simple disulfide: pdb=" SG CYS R 243 " - pdb=" SG CYS R 261 " distance=2.03 Simple disulfide: pdb=" SG CYS R 255 " - pdb=" SG CYS R 270 " distance=2.03 Simple disulfide: pdb=" SG CYS R 276 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 302 " distance=2.02 Simple disulfide: pdb=" SG CYS R 296 " - pdb=" SG CYS R 313 " distance=2.03 Simple disulfide: pdb=" SG CYS R 318 " - pdb=" SG CYS R 329 " distance=2.03 Simple disulfide: pdb=" SG CYS R 325 " - pdb=" SG CYS R 338 " distance=2.03 Simple disulfide: pdb=" SG CYS R 340 " - pdb=" SG CYS R 352 " distance=2.03 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 Links applied NAG-ASN " NAG A4601 " - " ASN A3336 " " NAG A4602 " - " ASN A2779 " " NAG A4603 " - " ASN A3101 " " NAG A4604 " - " ASN A3411 " " NAG A4605 " - " ASN A3465 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 745.8 milliseconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 27 sheets defined 18.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 1844 through 1846 No H-bonds generated for 'chain 'A' and resid 1844 through 1846' Processing helix chain 'A' and resid 1858 through 1862 Processing helix chain 'A' and resid 2042 through 2048 removed outlier: 4.144A pdb=" N GLU A2047 " --> pdb=" O ASP A2044 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A2048 " --> pdb=" O ALA A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2083 Processing helix chain 'A' and resid 2084 through 2094 removed outlier: 3.782A pdb=" N VAL A2090 " --> pdb=" O GLN A2086 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A2091 " --> pdb=" O THR A2087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A2094 " --> pdb=" O VAL A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2392 Processing helix chain 'A' and resid 2393 through 2406 removed outlier: 3.610A pdb=" N ASP A2398 " --> pdb=" O VAL A2394 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A2404 " --> pdb=" O ALA A2400 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A2406 " --> pdb=" O LYS A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2419 removed outlier: 4.236A pdb=" N ILE A2413 " --> pdb=" O PHE A2409 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A2414 " --> pdb=" O LYS A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2428 removed outlier: 3.985A pdb=" N ILE A2424 " --> pdb=" O LEU A2420 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A2425 " --> pdb=" O ASP A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2438 removed outlier: 4.026A pdb=" N VAL A2436 " --> pdb=" O TYR A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2468 removed outlier: 3.752A pdb=" N ILE A2443 " --> pdb=" O THR A2439 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A2444 " --> pdb=" O ASN A2440 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A2445 " --> pdb=" O ASP A2441 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A2446 " --> pdb=" O LYS A2442 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A2447 " --> pdb=" O ILE A2443 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY A2452 " --> pdb=" O GLN A2448 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A2453 " --> pdb=" O ARG A2449 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A2454 " --> pdb=" O LEU A2450 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A2455 " --> pdb=" O ASN A2451 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A2459 " --> pdb=" O GLN A2455 " (cutoff:3.500A) Proline residue: A2460 - end of helix removed outlier: 3.990A pdb=" N ALA A2463 " --> pdb=" O LEU A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.919A pdb=" N GLU B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 65 through 73 removed outlier: 4.060A pdb=" N TYR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.850A pdb=" N TRP B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.808A pdb=" N LEU B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 4.003A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 182 through 185 removed outlier: 4.555A pdb=" N ASP B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.567A pdb=" N LEU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.634A pdb=" N ALA B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.018A pdb=" N SER B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.385A pdb=" N GLU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.778A pdb=" N THR B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 353 removed outlier: 3.927A pdb=" N ALA B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 4.037A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 4.037A pdb=" N LEU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 removed outlier: 4.067A pdb=" N SER B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 removed outlier: 4.305A pdb=" N GLY B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 469 removed outlier: 3.678A pdb=" N GLY B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 518 removed outlier: 3.886A pdb=" N ALA B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.789A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 88 Processing helix chain 'R' and resid 125 through 127 No H-bonds generated for 'chain 'R' and resid 125 through 127' Processing helix chain 'R' and resid 137 through 142 removed outlier: 3.576A pdb=" N SER R 142 " --> pdb=" O SER R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 189 Processing helix chain 'R' and resid 211 through 215 Processing helix chain 'R' and resid 321 through 325 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.150A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 151 through 155 removed outlier: 5.105A pdb=" N LYS H 153 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU H 188 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 155 " --> pdb=" O TYR H 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AA5, first strand: chain 'A' and resid 1837 through 1843 removed outlier: 4.311A pdb=" N ALA A1853 " --> pdb=" O LEU A1868 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1868 " --> pdb=" O ALA A1853 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A1882 " --> pdb=" O ARG A1867 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A1883 " --> pdb=" O ASN A1894 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A1894 " --> pdb=" O THR A1883 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A1885 " --> pdb=" O PHE A1892 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A1906 " --> pdb=" O VAL A1899 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1917 " --> pdb=" O HIS A1923 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A1946 " --> pdb=" O HIS A1966 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1940 through 1941 Processing sheet with id=AA7, first strand: chain 'A' and resid 2004 through 2005 Processing sheet with id=AA8, first strand: chain 'A' and resid 2009 through 2015 removed outlier: 4.283A pdb=" N VAL A2055 " --> pdb=" O LYS A2763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A2775 " --> pdb=" O SER A2760 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A2762 " --> pdb=" O ALA A2773 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A2794 " --> pdb=" O ASN A2774 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A2814 " --> pdb=" O ILE A2789 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2822 through 2826 current: chain 'A' and resid 2835 through 2845 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2866 through 2868 current: chain 'A' and resid 2881 through 2883 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2881 through 2883 current: chain 'A' and resid 2900 through 2906 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2900 through 2906 current: chain 'A' and resid 2918 through 2920 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2918 through 2920 current: chain 'A' and resid 2939 through 2951 removed outlier: 3.642A pdb=" N LEU A2959 " --> pdb=" O LEU A2974 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A2961 " --> pdb=" O GLN A2972 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A2975 " --> pdb=" O GLU A2987 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A2987 " --> pdb=" O VAL A2975 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A3001 " --> pdb=" O ASP A3022 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A3022 " --> pdb=" O VAL A3001 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A3023 " --> pdb=" O LEU A3033 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A3025 " --> pdb=" O GLY A3031 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A3032 " --> pdb=" O ASN A3055 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A3055 " --> pdb=" O THR A3032 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A3034 " --> pdb=" O GLU A3053 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3066 through 3068 current: chain 'A' and resid 3084 through 3091 removed outlier: 3.550A pdb=" N GLU A3120 " --> pdb=" O LYS A3097 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3166 through 3168 current: chain 'A' and resid 3337 through 3344 removed outlier: 3.549A pdb=" N GLU A3355 " --> pdb=" O HIS A3365 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A3365 " --> pdb=" O GLU A3355 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A3357 " --> pdb=" O VAL A3363 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A3363 " --> pdb=" O PHE A3357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2769 through 2770 Processing sheet with id=AB1, first strand: chain 'A' and resid 3046 through 3047 Processing sheet with id=AB2, first strand: chain 'A' and resid 3382 through 3389 removed outlier: 3.605A pdb=" N ALA A3396 " --> pdb=" O THR A3384 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG A3386 " --> pdb=" O LYS A3394 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A3394 " --> pdb=" O ARG A3386 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A3388 " --> pdb=" O GLY A3392 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A3392 " --> pdb=" O THR A3388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3428 through 3433 removed outlier: 3.754A pdb=" N GLY A3475 " --> pdb=" O TYR A3462 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3472 through 3475 current: chain 'A' and resid 3490 through 3503 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3512 through 3515 current: chain 'A' and resid 3527 through 3529 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3527 through 3529 current: chain 'A' and resid 3543 through 3548 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3543 through 3548 current: chain 'A' and resid 3559 through 3563 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3559 through 3563 current: chain 'A' and resid 3577 through 3582 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3577 through 3582 current: chain 'A' and resid 3595 through 3602 removed outlier: 4.787A pdb=" N VAL A3602 " --> pdb=" O GLN A3618 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN A3618 " --> pdb=" O VAL A3602 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A3617 " --> pdb=" O GLU A3636 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A3636 " --> pdb=" O GLY A3617 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A3635 " --> pdb=" O SER A3646 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A3646 " --> pdb=" O ASN A3635 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A3661 " --> pdb=" O THR A3706 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A3706 " --> pdb=" O ILE A3661 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3702 through 3706 current: chain 'A' and resid 3882 through 3884 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.694A pdb=" N THR L 69 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 39 through 44 removed outlier: 6.143A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 51 through 55 current: chain 'L' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.850A pdb=" N PHE L 121 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU L 140 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 197 through 199 Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 64 removed outlier: 3.611A pdb=" N ILE B 61 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AC1, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 148 removed outlier: 9.309A pdb=" N SER B 146 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 226 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N LEU B 148 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ASN B 228 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 224 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 483 through 488 Processing sheet with id=AC4, first strand: chain 'B' and resid 522 through 526 Processing sheet with id=AC5, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.716A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.493A pdb=" N GLY N 10 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER N 122 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL N 12 " --> pdb=" O SER N 122 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 113 through 115 Processing sheet with id=AC8, first strand: chain 'R' and resid 152 through 154 Processing sheet with id=AC9, first strand: chain 'R' and resid 240 through 242 562 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.91 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: 5730 1.34 - 1.46: 4027 1.46 - 1.58: 7679 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 17537 Sorted by residual: bond pdb=" C VAL A2733 " pdb=" N PRO A2734 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.93e+00 bond pdb=" N ASN A3522 " pdb=" CA ASN A3522 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 bond pdb=" CA VAL L 201 " pdb=" CB VAL L 201 " ideal model delta sigma weight residual 1.550 1.541 0.010 1.03e-02 9.43e+03 9.19e-01 bond pdb=" CA GLN A2732 " pdb=" C GLN A2732 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.52e-02 4.33e+03 8.86e-01 bond pdb=" C TRP B 159 " pdb=" N PRO B 160 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.04e-01 ... (remaining 17532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 23592 2.22 - 4.43: 266 4.43 - 6.65: 27 6.65 - 8.86: 6 8.86 - 11.08: 5 Bond angle restraints: 23896 Sorted by residual: angle pdb=" CA LEU L 89 " pdb=" CB LEU L 89 " pdb=" CG LEU L 89 " ideal model delta sigma weight residual 116.30 127.38 -11.08 3.50e+00 8.16e-02 1.00e+01 angle pdb=" N ALA R 141 " pdb=" CA ALA R 141 " pdb=" C ALA R 141 " ideal model delta sigma weight residual 114.56 110.60 3.96 1.27e+00 6.20e-01 9.74e+00 angle pdb=" C2 NAG A4603 " pdb=" N2 NAG A4603 " pdb=" C7 NAG A4603 " ideal model delta sigma weight residual 124.56 133.91 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" CB MET A2843 " pdb=" CG MET A2843 " pdb=" SD MET A2843 " ideal model delta sigma weight residual 112.70 121.59 -8.89 3.00e+00 1.11e-01 8.79e+00 angle pdb=" CA LEU A3062 " pdb=" CB LEU A3062 " pdb=" CG LEU A3062 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.27e+00 ... (remaining 23891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9430 17.66 - 35.32: 877 35.32 - 52.99: 120 52.99 - 70.65: 32 70.65 - 88.31: 11 Dihedral angle restraints: 10470 sinusoidal: 3724 harmonic: 6746 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 166.50 -73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS R 68 " pdb=" SG CYS R 68 " pdb=" SG CYS R 82 " pdb=" CB CYS R 82 " ideal model delta sinusoidal sigma weight residual 93.00 160.97 -67.97 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CB CYS R 296 " pdb=" SG CYS R 296 " pdb=" SG CYS R 313 " pdb=" CB CYS R 313 " ideal model delta sinusoidal sigma weight residual 93.00 150.92 -57.92 1 1.00e+01 1.00e-02 4.50e+01 ... (remaining 10467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2577 0.079 - 0.158: 211 0.158 - 0.238: 2 0.238 - 0.317: 1 0.317 - 0.396: 1 Chirality restraints: 2792 Sorted by residual: chirality pdb=" C1 NAG A4604 " pdb=" ND2 ASN A3411 " pdb=" C2 NAG A4604 " pdb=" O5 NAG A4604 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C2 NAG A4603 " pdb=" C1 NAG A4603 " pdb=" C3 NAG A4603 " pdb=" N2 NAG A4603 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG A4601 " pdb=" ND2 ASN A3336 " pdb=" C2 NAG A4601 " pdb=" O5 NAG A4601 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2789 not shown) Planarity restraints: 3123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A3465 " -0.020 2.00e-02 2.50e+03 1.95e-02 4.74e+00 pdb=" CG ASN A3465 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A3465 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A3465 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A4605 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1973 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A1974 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1974 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1974 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 161 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO R 162 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " -0.027 5.00e-02 4.00e+02 ... (remaining 3120 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 809 2.70 - 3.25: 19311 3.25 - 3.80: 29223 3.80 - 4.35: 35888 4.35 - 4.90: 56930 Nonbonded interactions: 142161 Sorted by model distance: nonbonded pdb=" OG SER R 326 " pdb=" O LEU R 339 " model vdw 2.153 3.040 nonbonded pdb=" O SER A3561 " pdb=" OG1 THR A3588 " model vdw 2.172 3.040 nonbonded pdb=" OG SER R 123 " pdb=" OE1 GLN R 125 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR A3489 " pdb=" O ARG R 303 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR A3384 " pdb=" O ALA A3396 " model vdw 2.190 3.040 ... (remaining 142156 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.002 0.052 17568 Z= 0.111 Angle : 0.609 11.078 23963 Z= 0.301 Chirality : 0.042 0.396 2792 Planarity : 0.004 0.050 3118 Dihedral : 13.841 88.312 6022 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.18), residues: 2272 helix: -0.22 (0.31), residues: 282 sheet: -1.53 (0.18), residues: 856 loop : -1.03 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3386 TYR 0.019 0.001 TYR R 336 PHE 0.019 0.001 PHE B 259 TRP 0.020 0.001 TRP A3087 HIS 0.004 0.001 HIS R 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (17537) covalent geometry : angle 0.59306 / 0.30 (23896) SS BOND : bond 0.00247 / 0.13 ( 26) SS BOND : angle 1.05500 / 0.60 ( 52) hydrogen bonds : bond 0.26709 / 18.16 ( 562) hydrogen bonds : angle 11.12964 / 7.56 ( 1476) link_NAG-ASN : bond 0.00833 / 0.42 ( 5) link_NAG-ASN : angle 5.31011 / 3.10 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3058 VAL cc_start: 0.9202 (p) cc_final: 0.8808 (p) REVERT: A 3060 PHE cc_start: 0.8805 (m-80) cc_final: 0.8580 (m-80) REVERT: B 225 MET cc_start: 0.8465 (pmm) cc_final: 0.8050 (pmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1080 time to fit residues: 17.4744 Evaluate side-chains 77 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2765 GLN ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3118 ASN A3167 GLN ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.057145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.043517 restraints weight = 157523.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.044407 restraints weight = 96593.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.044992 restraints weight = 70145.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045374 restraints weight = 56884.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.045586 restraints weight = 49683.675| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17568 Z= 0.245 Angle : 0.679 10.752 23963 Z= 0.358 Chirality : 0.044 0.479 2792 Planarity : 0.005 0.053 3118 Dihedral : 5.491 54.255 2519 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.28 % Allowed : 9.54 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.18), residues: 2272 helix: -0.41 (0.28), residues: 321 sheet: -1.75 (0.17), residues: 866 loop : -1.26 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 60 TYR 0.018 0.002 TYR H 95 PHE 0.022 0.002 PHE R 126 TRP 0.027 0.002 TRP A3087 HIS 0.006 0.001 HIS A3603 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (17537) covalent geometry : angle 0.67007 / 0.36 (23896) SS BOND : bond 0.00351 / 0.20 ( 26) SS BOND : angle 1.06375 / 0.66 ( 52) hydrogen bonds : bond 0.05467 / 3.68 ( 562) hydrogen bonds : angle 8.40980 / 5.73 ( 1476) link_NAG-ASN : bond 0.00624 / 0.32 ( 5) link_NAG-ASN : angle 4.18983 / 2.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3167 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8497 (pp30) REVERT: A 3438 MET cc_start: 0.8763 (tmm) cc_final: 0.8488 (tmm) REVERT: R 264 MET cc_start: 0.8728 (mmp) cc_final: 0.8172 (mmp) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1052 time to fit residues: 16.5805 Evaluate side-chains 74 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 193 optimal weight: 0.5980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2945 GLN ** A3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 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 = 0.3652 r_free = 0.3652 target = 0.057848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044268 restraints weight = 157963.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.045202 restraints weight = 95711.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045815 restraints weight = 68710.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046221 restraints weight = 55194.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.046463 restraints weight = 47973.798| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17568 Z= 0.188 Angle : 0.650 11.001 23963 Z= 0.336 Chirality : 0.045 0.479 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.503 54.076 2519 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.18), residues: 2272 helix: -0.43 (0.28), residues: 330 sheet: -1.80 (0.17), residues: 870 loop : -1.31 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3092 TYR 0.014 0.002 TYR H 95 PHE 0.028 0.002 PHE B 424 TRP 0.022 0.002 TRP R 165 HIS 0.006 0.001 HIS A3114 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (17537) covalent geometry : angle 0.64024 / 0.33 (23896) SS BOND : bond 0.00285 / 0.15 ( 26) SS BOND : angle 1.28034 / 0.74 ( 52) hydrogen bonds : bond 0.04287 / 2.87 ( 562) hydrogen bonds : angle 7.73621 / 5.28 ( 1476) link_NAG-ASN : bond 0.00639 / 0.32 ( 5) link_NAG-ASN : angle 4.01561 / 2.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 TYR cc_start: 0.8774 (m-80) cc_final: 0.8288 (m-80) REVERT: R 259 TYR cc_start: 0.7685 (m-10) cc_final: 0.7461 (m-80) REVERT: R 264 MET cc_start: 0.8721 (mmp) cc_final: 0.8191 (mmp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1020 time to fit residues: 15.9172 Evaluate side-chains 73 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2765 GLN A2891 HIS ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.057755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044164 restraints weight = 158608.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.045095 restraints weight = 96345.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045709 restraints weight = 69245.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.046110 restraints weight = 55531.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.046327 restraints weight = 48333.390| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17568 Z= 0.172 Angle : 0.638 10.965 23963 Z= 0.328 Chirality : 0.044 0.470 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.439 54.134 2519 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.11 % Allowed : 6.36 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.18), residues: 2272 helix: -0.48 (0.28), residues: 339 sheet: -1.87 (0.17), residues: 873 loop : -1.29 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3092 TYR 0.017 0.002 TYR A3074 PHE 0.029 0.002 PHE B 424 TRP 0.023 0.002 TRP A3633 HIS 0.005 0.001 HIS A3114 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (17537) covalent geometry : angle 0.62975 / 0.33 (23896) SS BOND : bond 0.00402 / 0.26 ( 26) SS BOND : angle 1.08184 / 0.65 ( 52) hydrogen bonds : bond 0.03725 / 2.49 ( 562) hydrogen bonds : angle 7.26004 / 4.95 ( 1476) link_NAG-ASN : bond 0.00660 / 0.32 ( 5) link_NAG-ASN : angle 3.91392 / 2.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1900 MET cc_start: 0.9158 (mpp) cc_final: 0.8810 (mpp) REVERT: B 333 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7724 (p0) REVERT: B 342 TYR cc_start: 0.8832 (m-80) cc_final: 0.8380 (m-80) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.1092 time to fit residues: 17.4371 Evaluate side-chains 75 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 46 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 130 optimal weight: 0.0770 chunk 129 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3410 HIS ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 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 = 0.3652 r_free = 0.3652 target = 0.057925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.044487 restraints weight = 156866.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.045722 restraints weight = 100479.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.046010 restraints weight = 63424.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.046168 restraints weight = 58298.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046203 restraints weight = 51979.662| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17568 Z= 0.180 Angle : 0.646 10.857 23963 Z= 0.332 Chirality : 0.044 0.464 2792 Planarity : 0.004 0.060 3118 Dihedral : 5.443 54.043 2519 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.18), residues: 2272 helix: -0.48 (0.28), residues: 333 sheet: -1.93 (0.17), residues: 870 loop : -1.31 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2012 TYR 0.019 0.002 TYR A3074 PHE 0.017 0.002 PHE A2057 TRP 0.021 0.002 TRP R 305 HIS 0.005 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (17537) covalent geometry : angle 0.63701 / 0.33 (23896) SS BOND : bond 0.00273 / 0.15 ( 26) SS BOND : angle 1.22491 / 0.71 ( 52) hydrogen bonds : bond 0.03610 / 2.40 ( 562) hydrogen bonds : angle 7.09083 / 4.81 ( 1476) link_NAG-ASN : bond 0.00617 / 0.30 ( 5) link_NAG-ASN : angle 3.87471 / 2.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9398 (mmm) cc_final: 0.9175 (mmm) REVERT: A 3007 MET cc_start: 0.9472 (tmm) cc_final: 0.9193 (tmm) REVERT: B 342 TYR cc_start: 0.8804 (m-80) cc_final: 0.8372 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1016 time to fit residues: 15.8889 Evaluate side-chains 69 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 222 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 127 optimal weight: 0.3980 chunk 170 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2745 HIS ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2982 ASN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3410 HIS ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.055232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041523 restraints weight = 164432.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042328 restraints weight = 104356.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.042848 restraints weight = 77582.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043176 restraints weight = 63865.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043379 restraints weight = 56551.769| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.187 17568 Z= 0.447 Angle : 0.912 10.915 23963 Z= 0.476 Chirality : 0.050 0.519 2792 Planarity : 0.006 0.061 3118 Dihedral : 6.588 51.794 2519 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.18), residues: 2272 helix: -0.96 (0.27), residues: 334 sheet: -2.26 (0.17), residues: 869 loop : -1.60 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 300 TYR 0.036 0.004 TYR H 95 PHE 0.041 0.004 PHE A3343 TRP 0.051 0.005 TRP A3633 HIS 0.014 0.003 HIS R 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.45 (17537) covalent geometry : angle 0.90254 / 0.47 (23896) SS BOND : bond 0.00487 / 0.31 ( 26) SS BOND : angle 1.88313 / 1.09 ( 52) hydrogen bonds : bond 0.04918 / 3.27 ( 562) hydrogen bonds : angle 7.81489 / 5.29 ( 1476) link_NAG-ASN : bond 0.00974 / 0.48 ( 5) link_NAG-ASN : angle 4.44809 / 2.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9409 (mmm) cc_final: 0.9134 (mmm) REVERT: A 3007 MET cc_start: 0.9409 (tmm) cc_final: 0.9192 (tmm) REVERT: B 342 TYR cc_start: 0.8848 (m-80) cc_final: 0.8463 (m-80) REVERT: R 264 MET cc_start: 0.8731 (mmp) cc_final: 0.8525 (tpt) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1105 time to fit residues: 14.8775 Evaluate side-chains 62 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 157 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.0050 chunk 101 optimal weight: 0.5980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1910 HIS A2861 HIS A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 515 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.057684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044066 restraints weight = 158232.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044998 restraints weight = 95338.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.045604 restraints weight = 68325.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.046006 restraints weight = 54875.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046271 restraints weight = 47829.877| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17568 Z= 0.162 Angle : 0.676 11.382 23963 Z= 0.347 Chirality : 0.046 0.463 2792 Planarity : 0.004 0.057 3118 Dihedral : 5.758 53.019 2519 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.18), residues: 2272 helix: -0.76 (0.28), residues: 346 sheet: -2.06 (0.17), residues: 876 loop : -1.45 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A3092 TYR 0.023 0.002 TYR A3074 PHE 0.030 0.002 PHE B 424 TRP 0.027 0.002 TRP R 305 HIS 0.005 0.001 HIS A3365 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (17537) covalent geometry : angle 0.66389 / 0.34 (23896) SS BOND : bond 0.00307 / 0.17 ( 26) SS BOND : angle 1.73568 / 0.95 ( 52) hydrogen bonds : bond 0.03536 / 2.37 ( 562) hydrogen bonds : angle 7.17772 / 4.83 ( 1476) link_NAG-ASN : bond 0.00689 / 0.33 ( 5) link_NAG-ASN : angle 4.14013 / 2.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9414 (mmm) cc_final: 0.9033 (mmm) REVERT: A 3007 MET cc_start: 0.9351 (tmm) cc_final: 0.9094 (tmm) REVERT: L 166 GLU cc_start: 0.9280 (pm20) cc_final: 0.8780 (pm20) REVERT: B 342 TYR cc_start: 0.8808 (m-80) cc_final: 0.8327 (m-80) REVERT: B 420 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8361 (pp30) REVERT: R 264 MET cc_start: 0.8814 (mmp) cc_final: 0.8309 (tpt) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.0955 time to fit residues: 14.3050 Evaluate side-chains 70 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 181 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** 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 = 0.3623 r_free = 0.3623 target = 0.056811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043005 restraints weight = 158415.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.043916 restraints weight = 96072.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044502 restraints weight = 69473.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.044899 restraints weight = 56293.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045152 restraints weight = 48959.475| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17568 Z= 0.248 Angle : 0.725 11.712 23963 Z= 0.374 Chirality : 0.046 0.482 2792 Planarity : 0.005 0.057 3118 Dihedral : 5.871 53.238 2519 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.18), residues: 2272 helix: -0.67 (0.28), residues: 335 sheet: -2.14 (0.17), residues: 873 loop : -1.42 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 67 TYR 0.022 0.002 TYR A3520 PHE 0.022 0.002 PHE A3343 TRP 0.033 0.003 TRP R 305 HIS 0.007 0.002 HIS R 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (17537) covalent geometry : angle 0.71487 / 0.37 (23896) SS BOND : bond 0.00313 / 0.19 ( 26) SS BOND : angle 1.58752 / 0.89 ( 52) hydrogen bonds : bond 0.03850 / 2.59 ( 562) hydrogen bonds : angle 7.29542 / 4.92 ( 1476) link_NAG-ASN : bond 0.00602 / 0.29 ( 5) link_NAG-ASN : angle 4.05167 / 2.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9411 (mmm) cc_final: 0.9043 (mmm) REVERT: A 3007 MET cc_start: 0.9357 (tmm) cc_final: 0.9057 (tmm) REVERT: B 342 TYR cc_start: 0.8807 (m-80) cc_final: 0.8360 (m-80) REVERT: R 264 MET cc_start: 0.8716 (mmp) cc_final: 0.8395 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1010 time to fit residues: 14.2790 Evaluate side-chains 67 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 25 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 179 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3595 GLN ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN B 366 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.058291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.044593 restraints weight = 158300.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.045548 restraints weight = 95181.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046172 restraints weight = 68163.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.046566 restraints weight = 54630.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046810 restraints weight = 47606.842| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17568 Z= 0.135 Angle : 0.670 11.163 23963 Z= 0.337 Chirality : 0.045 0.439 2792 Planarity : 0.004 0.054 3118 Dihedral : 5.542 54.013 2519 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.06 % Allowed : 1.02 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.18), residues: 2272 helix: -0.62 (0.28), residues: 348 sheet: -2.02 (0.17), residues: 875 loop : -1.31 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3527 TYR 0.023 0.001 TYR A3074 PHE 0.019 0.001 PHE R 86 TRP 0.018 0.002 TRP R 305 HIS 0.004 0.001 HIS A1944 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17537) covalent geometry : angle 0.65344 / 0.33 (23896) SS BOND : bond 0.00260 / 0.14 ( 26) SS BOND : angle 1.40562 / 0.79 ( 52) hydrogen bonds : bond 0.03310 / 2.24 ( 562) hydrogen bonds : angle 6.93580 / 4.67 ( 1476) link_NAG-ASN : bond 0.00839 / 0.42 ( 5) link_NAG-ASN : angle 5.48311 / 3.11 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9426 (mmm) cc_final: 0.9022 (mmm) REVERT: A 3007 MET cc_start: 0.9337 (tmm) cc_final: 0.9010 (tmm) REVERT: A 3438 MET cc_start: 0.8757 (tmm) cc_final: 0.8368 (tmm) REVERT: B 342 TYR cc_start: 0.8809 (m-80) cc_final: 0.8317 (m-80) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1034 time to fit residues: 15.6999 Evaluate side-chains 71 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 87 optimal weight: 0.9990 chunk 227 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 123 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3606 GLN ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN B 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.058333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046666 restraints weight = 159698.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046811 restraints weight = 106102.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.046813 restraints weight = 77414.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.046987 restraints weight = 73077.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.047027 restraints weight = 66976.960| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17568 Z= 0.118 Angle : 0.651 10.852 23963 Z= 0.325 Chirality : 0.045 0.421 2792 Planarity : 0.004 0.064 3118 Dihedral : 5.267 55.461 2519 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.18), residues: 2272 helix: -0.57 (0.27), residues: 365 sheet: -1.94 (0.17), residues: 867 loop : -1.35 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1867 TYR 0.021 0.001 TYR A3177 PHE 0.019 0.001 PHE B 259 TRP 0.017 0.002 TRP R 214 HIS 0.007 0.001 HIS R 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17537) covalent geometry : angle 0.63731 / 0.32 (23896) SS BOND : bond 0.00255 / 0.15 ( 26) SS BOND : angle 1.27533 / 0.74 ( 52) hydrogen bonds : bond 0.03115 / 2.11 ( 562) hydrogen bonds : angle 6.58098 / 4.44 ( 1476) link_NAG-ASN : bond 0.00874 / 0.44 ( 5) link_NAG-ASN : angle 5.00505 / 2.83 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9440 (mmm) cc_final: 0.9015 (mmm) REVERT: A 3007 MET cc_start: 0.9314 (tmm) cc_final: 0.8875 (tmm) REVERT: A 3438 MET cc_start: 0.8715 (tmm) cc_final: 0.8455 (tmm) REVERT: L 165 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5646 (tm-30) REVERT: B 342 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1029 time to fit residues: 16.3031 Evaluate side-chains 75 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 175 optimal weight: 0.0870 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN ** B 119 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 = 0.3663 r_free = 0.3663 target = 0.058227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.045292 restraints weight = 158095.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.046110 restraints weight = 103093.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.046357 restraints weight = 71517.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046531 restraints weight = 66215.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046503 restraints weight = 58765.213| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17568 Z= 0.156 Angle : 0.646 10.535 23963 Z= 0.326 Chirality : 0.044 0.426 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.341 54.343 2519 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 2272 helix: -0.42 (0.28), residues: 354 sheet: -1.96 (0.17), residues: 858 loop : -1.33 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3527 TYR 0.014 0.001 TYR A3177 PHE 0.019 0.002 PHE B 424 TRP 0.022 0.002 TRP R 305 HIS 0.006 0.001 HIS R 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17537) covalent geometry : angle 0.63330 / 0.32 (23896) SS BOND : bond 0.00258 / 0.15 ( 26) SS BOND : angle 1.22823 / 0.71 ( 52) hydrogen bonds : bond 0.03193 / 2.15 ( 562) hydrogen bonds : angle 6.56864 / 4.43 ( 1476) link_NAG-ASN : bond 0.00741 / 0.39 ( 5) link_NAG-ASN : angle 4.69642 / 2.64 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3057.24 seconds wall clock time: 53 minutes 43.64 seconds (3223.64 seconds total)