Starting phenix.real_space_refine on Tue Jan 21 22:13:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_44450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_44450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_44450.map" model { file = "/net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_44450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bde_44450/01_2025/9bde_44450.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 9} 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, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG: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, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 11} 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, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 9.92, per 1000 atoms: 0.58 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: 4.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.54 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: 7.36 Time building geometry restraints manager: 5.20 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: 2.480 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 17537 Z= 0.154 Angle : 0.593 11.078 23896 Z= 0.297 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 : 18.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (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 TRP 0.020 0.001 TRP A3087 HIS 0.004 0.001 HIS R 211 PHE 0.019 0.001 PHE B 259 TYR 0.019 0.001 TYR R 336 ARG 0.003 0.000 ARG A3386 *********************** 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 : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3058 VAL cc_start: 0.9202 (p) cc_final: 0.8812 (p) REVERT: A 3060 PHE cc_start: 0.8805 (m-80) cc_final: 0.8575 (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: 0.2984 time to fit residues: 47.7770 Evaluate side-chains 76 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3118 ASN ** A3167 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 366 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.056313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.042505 restraints weight = 160811.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043393 restraints weight = 98659.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.043971 restraints weight = 71693.228| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 17537 Z= 0.469 Angle : 0.750 9.409 23896 Z= 0.399 Chirality : 0.045 0.502 2792 Planarity : 0.005 0.055 3118 Dihedral : 5.773 55.379 2519 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.57 % Allowed : 10.11 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.18), residues: 2272 helix: -0.62 (0.28), residues: 327 sheet: -1.86 (0.17), residues: 863 loop : -1.32 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A3087 HIS 0.008 0.002 HIS A3479 PHE 0.034 0.002 PHE R 126 TYR 0.025 0.002 TYR H 95 ARG 0.007 0.001 ARG A1867 *********************** 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 99 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8357 (mmp) cc_final: 0.8023 (mmm) REVERT: A 3438 MET cc_start: 0.8807 (tmm) cc_final: 0.8462 (tmm) REVERT: R 264 MET cc_start: 0.8648 (mmp) cc_final: 0.8432 (mmt) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.2696 time to fit residues: 43.6985 Evaluate side-chains 72 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2945 GLN A3073 ASN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.057828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.044653 restraints weight = 163026.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045603 restraints weight = 97825.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.046229 restraints weight = 69968.760| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17537 Z= 0.199 Angle : 0.627 9.345 23896 Z= 0.324 Chirality : 0.045 0.466 2792 Planarity : 0.004 0.054 3118 Dihedral : 5.450 54.215 2519 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.18), residues: 2272 helix: -0.53 (0.28), residues: 326 sheet: -1.84 (0.17), residues: 876 loop : -1.20 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 305 HIS 0.005 0.001 HIS A1944 PHE 0.032 0.002 PHE B 424 TYR 0.021 0.001 TYR A3177 ARG 0.012 0.001 ARG A3092 *********************** 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 97 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3395 LEU cc_start: 0.9350 (tp) cc_final: 0.9094 (mm) REVERT: B 342 TYR cc_start: 0.8676 (m-80) cc_final: 0.8235 (m-80) REVERT: R 264 MET cc_start: 0.8587 (mmp) cc_final: 0.8272 (mmt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2682 time to fit residues: 43.6116 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 : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 57 optimal weight: 0.0020 chunk 198 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2891 HIS ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 429 ASN ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.057359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044017 restraints weight = 157947.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045294 restraints weight = 101485.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.045362 restraints weight = 64830.840| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17537 Z= 0.294 Angle : 0.656 10.704 23896 Z= 0.340 Chirality : 0.044 0.486 2792 Planarity : 0.004 0.054 3118 Dihedral : 5.540 53.859 2519 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 5.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 2272 helix: -0.47 (0.28), residues: 319 sheet: -1.97 (0.17), residues: 869 loop : -1.23 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP R 165 HIS 0.006 0.001 HIS R 285 PHE 0.020 0.002 PHE B 195 TYR 0.017 0.002 TYR A3074 ARG 0.006 0.001 ARG A3092 *********************** 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 91 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1900 MET cc_start: 0.9263 (mpp) cc_final: 0.9038 (mpp) REVERT: A 3007 MET cc_start: 0.9556 (tmm) cc_final: 0.9296 (tmm) REVERT: A 3438 MET cc_start: 0.8967 (tmm) cc_final: 0.8668 (tmm) REVERT: B 342 TYR cc_start: 0.8754 (m-80) cc_final: 0.8303 (m-80) REVERT: R 264 MET cc_start: 0.8628 (mmp) cc_final: 0.8313 (mmt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2594 time to fit residues: 40.3756 Evaluate side-chains 68 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 183 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 154 optimal weight: 0.0040 chunk 32 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2745 HIS ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 333 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.057756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.044370 restraints weight = 158813.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.045203 restraints weight = 100116.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045750 restraints weight = 73789.781| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17537 Z= 0.249 Angle : 0.631 9.416 23896 Z= 0.326 Chirality : 0.044 0.466 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.477 53.832 2519 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 2272 helix: -0.52 (0.28), residues: 338 sheet: -1.97 (0.17), residues: 872 loop : -1.26 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 165 HIS 0.005 0.001 HIS A3114 PHE 0.017 0.002 PHE A2057 TYR 0.019 0.002 TYR A3074 ARG 0.006 0.001 ARG N 67 *********************** 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: 2 poor density : 93 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9400 (mmm) cc_final: 0.9187 (mmm) REVERT: A 3007 MET cc_start: 0.9493 (tmm) cc_final: 0.9238 (tmm) REVERT: B 333 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7762 (p0) REVERT: B 342 TYR cc_start: 0.8755 (m-80) cc_final: 0.8287 (m-80) REVERT: R 264 MET cc_start: 0.8634 (mmp) cc_final: 0.8334 (mmt) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.2525 time to fit residues: 41.2297 Evaluate side-chains 72 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 124 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1886 ASN A2945 GLN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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** ** 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 = 0.3670 r_free = 0.3670 target = 0.058476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.045081 restraints weight = 156990.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046333 restraints weight = 96346.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046617 restraints weight = 60495.428| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17537 Z= 0.186 Angle : 0.608 9.392 23896 Z= 0.310 Chirality : 0.044 0.447 2792 Planarity : 0.004 0.061 3118 Dihedral : 5.242 54.506 2519 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2272 helix: -0.45 (0.28), residues: 341 sheet: -1.88 (0.17), residues: 868 loop : -1.23 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 165 HIS 0.004 0.001 HIS R 285 PHE 0.018 0.001 PHE A2057 TYR 0.022 0.001 TYR A3074 ARG 0.004 0.000 ARG A3092 *********************** 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 98 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9421 (mmm) cc_final: 0.9105 (mmm) REVERT: A 3007 MET cc_start: 0.9423 (tmm) cc_final: 0.9108 (tmm) REVERT: B 342 TYR cc_start: 0.8837 (m-80) cc_final: 0.8385 (m-80) REVERT: R 264 MET cc_start: 0.8604 (mmp) cc_final: 0.8253 (mmt) REVERT: R 342 ASP cc_start: 0.7096 (t0) cc_final: 0.6893 (t0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2726 time to fit residues: 44.5354 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 : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 12 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.058256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.045559 restraints weight = 159647.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.046064 restraints weight = 106324.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046248 restraints weight = 75560.009| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17537 Z= 0.201 Angle : 0.613 9.394 23896 Z= 0.314 Chirality : 0.044 0.458 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.203 54.621 2519 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2272 helix: -0.40 (0.28), residues: 341 sheet: -1.88 (0.17), residues: 866 loop : -1.20 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 165 HIS 0.014 0.001 HIS A3410 PHE 0.017 0.001 PHE A2057 TYR 0.051 0.002 TYR A3520 ARG 0.002 0.000 ARG A3092 *********************** 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 97 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9454 (mmm) cc_final: 0.9107 (mmm) REVERT: A 3007 MET cc_start: 0.9419 (tmm) cc_final: 0.9075 (tmm) REVERT: B 342 TYR cc_start: 0.8719 (m-80) cc_final: 0.8342 (m-80) REVERT: R 264 MET cc_start: 0.8577 (mmp) cc_final: 0.8184 (mmt) REVERT: R 298 MET cc_start: 0.7384 (mpp) cc_final: 0.7000 (mpp) REVERT: R 342 ASP cc_start: 0.7109 (t0) cc_final: 0.6899 (t0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2648 time to fit residues: 43.0558 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 : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 219 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2451 ASN ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2982 ASN ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3176 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.056047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042255 restraints weight = 162870.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.043083 restraints weight = 101949.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043616 restraints weight = 75179.523| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 17537 Z= 0.483 Angle : 0.800 11.684 23896 Z= 0.418 Chirality : 0.047 0.495 2792 Planarity : 0.005 0.060 3118 Dihedral : 6.135 52.176 2519 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.18), residues: 2272 helix: -0.64 (0.28), residues: 329 sheet: -2.21 (0.17), residues: 881 loop : -1.42 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP R 305 HIS 0.013 0.003 HIS R 285 PHE 0.034 0.003 PHE A3343 TYR 0.055 0.003 TYR A3520 ARG 0.005 0.001 ARG A2969 *********************** 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 83 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9446 (mmm) cc_final: 0.9071 (mmm) REVERT: A 3007 MET cc_start: 0.9402 (tmm) cc_final: 0.9069 (tmm) REVERT: L 166 GLU cc_start: 0.9405 (pm20) cc_final: 0.9067 (pm20) REVERT: B 342 TYR cc_start: 0.8797 (m-80) cc_final: 0.8383 (m-80) REVERT: R 264 MET cc_start: 0.8678 (mmp) cc_final: 0.8395 (mmt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2644 time to fit residues: 37.0538 Evaluate side-chains 66 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 149 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 30 optimal weight: 0.0010 chunk 4 optimal weight: 0.7980 chunk 99 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2861 HIS ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.058083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.046687 restraints weight = 159590.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.046696 restraints weight = 104001.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046569 restraints weight = 86766.610| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17537 Z= 0.180 Angle : 0.662 11.067 23896 Z= 0.334 Chirality : 0.046 0.415 2792 Planarity : 0.004 0.056 3118 Dihedral : 5.426 54.244 2519 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 2272 helix: -0.53 (0.28), residues: 344 sheet: -1.96 (0.17), residues: 868 loop : -1.26 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 165 HIS 0.006 0.001 HIS A1944 PHE 0.024 0.001 PHE B 259 TYR 0.037 0.002 TYR A3520 ARG 0.003 0.000 ARG R 300 *********************** 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 96 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9421 (mmm) cc_final: 0.9102 (mmm) REVERT: A 3007 MET cc_start: 0.9302 (tmm) cc_final: 0.8952 (tmm) REVERT: L 3 MET cc_start: 0.7963 (tmm) cc_final: 0.7754 (tmm) REVERT: B 342 TYR cc_start: 0.8424 (m-80) cc_final: 0.8183 (m-80) REVERT: B 370 MET cc_start: 0.7455 (mpp) cc_final: 0.6868 (mpp) REVERT: R 264 MET cc_start: 0.8198 (mmp) cc_final: 0.7789 (mmt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2687 time to fit residues: 43.0179 Evaluate side-chains 72 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 129 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.058414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045001 restraints weight = 157953.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.046205 restraints weight = 102030.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046333 restraints weight = 67092.714| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17537 Z= 0.193 Angle : 0.636 11.204 23896 Z= 0.321 Chirality : 0.044 0.423 2792 Planarity : 0.004 0.055 3118 Dihedral : 5.275 54.889 2519 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2272 helix: -0.58 (0.28), residues: 356 sheet: -1.94 (0.17), residues: 865 loop : -1.24 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 165 HIS 0.004 0.001 HIS R 285 PHE 0.018 0.001 PHE B 259 TYR 0.032 0.001 TYR A3520 ARG 0.003 0.000 ARG N 45 ********************** 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 94 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3007 MET cc_start: 0.9404 (tmm) cc_final: 0.8964 (tmm) REVERT: A 3438 MET cc_start: 0.8788 (tmm) cc_final: 0.8411 (tmm) REVERT: B 342 TYR cc_start: 0.8844 (m-80) cc_final: 0.8376 (m-80) REVERT: R 264 MET cc_start: 0.8375 (mmp) cc_final: 0.8064 (mmt) REVERT: R 298 MET cc_start: 0.7477 (mpp) cc_final: 0.7227 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2648 time to fit residues: 41.7304 Evaluate side-chains 75 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 125 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3167 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.057550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043734 restraints weight = 158727.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.044654 restraints weight = 96840.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.045242 restraints weight = 69902.118| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17537 Z= 0.287 Angle : 0.670 11.047 23896 Z= 0.344 Chirality : 0.045 0.449 2792 Planarity : 0.004 0.056 3118 Dihedral : 5.536 53.750 2519 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.18), residues: 2272 helix: -0.63 (0.28), residues: 350 sheet: -1.99 (0.17), residues: 886 loop : -1.30 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 305 HIS 0.017 0.002 HIS A3410 PHE 0.019 0.002 PHE A3343 TYR 0.035 0.002 TYR A3520 ARG 0.006 0.001 ARG A1867 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.64 seconds wall clock time: 97 minutes 5.58 seconds (5825.58 seconds total)