Starting phenix.real_space_refine on Sun Jun 15 15:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bde_44450/06_2025/9bde_44450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bde_44450/06_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_44450/06_2025/9bde_44450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bde_44450/06_2025/9bde_44450.map" model { file = "/net/cci-nas-00/data/ceres_data/9bde_44450/06_2025/9bde_44450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bde_44450/06_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-5710/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: 9.83, per 1000 atoms: 0.57 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: 4.05 Conformation dependent library (CDL) restraints added in 2.2 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: 2.32 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: 7.54 Time building geometry restraints manager: 4.86 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: 2.860 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.940 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- 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 17568 Z= 0.111 Angle : 0.609 11.078 23963 Z= 0.301 Chirality : 0.042 0.396 2792 Planarity : 0.004 0.050 3118 Dihedral : 13.841 88.312 6022 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.99 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 5) link_NAG-ASN : angle 5.31011 ( 15) hydrogen bonds : bond 0.26709 ( 562) hydrogen bonds : angle 11.12964 ( 1476) SS BOND : bond 0.00247 ( 26) SS BOND : angle 1.05500 ( 52) covalent geometry : bond 0.00229 (17537) covalent geometry : angle 0.59306 (23896) *********************** 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 : 1.763 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: 0.2729 time to fit residues: 43.8957 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 : 1.772 ------------------------------------------------------------------------------- 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: 7.9990 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 = 71)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.042515 restraints weight = 160811.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043398 restraints weight = 98574.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043936 restraints weight = 71568.862| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 17568 Z= 0.343 Angle : 0.759 10.693 23963 Z= 0.401 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 5) link_NAG-ASN : angle 4.36202 ( 15) hydrogen bonds : bond 0.05628 ( 562) hydrogen bonds : angle 8.64048 ( 1476) SS BOND : bond 0.00431 ( 26) SS BOND : angle 1.19487 ( 52) covalent geometry : bond 0.00713 (17537) covalent geometry : angle 0.74995 (23896) *********************** 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 : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8360 (mmp) cc_final: 0.8027 (mmm) REVERT: A 3438 MET cc_start: 0.8812 (tmm) cc_final: 0.8464 (tmm) REVERT: R 264 MET cc_start: 0.8651 (mmp) cc_final: 0.8438 (mmt) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.2637 time to fit residues: 43.2050 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 : 1.826 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 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: 7.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.058198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.044644 restraints weight = 158700.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.045569 restraints weight = 95839.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.046185 restraints weight = 69015.486| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17568 Z= 0.151 Angle : 0.642 11.215 23963 Z= 0.329 Chirality : 0.045 0.471 2792 Planarity : 0.004 0.054 3118 Dihedral : 5.502 53.939 2519 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -0.54 (0.28), residues: 329 sheet: -1.84 (0.17), residues: 872 loop : -1.24 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 305 HIS 0.006 0.001 HIS A2967 PHE 0.030 0.002 PHE B 424 TYR 0.021 0.002 TYR A3177 ARG 0.012 0.001 ARG A3092 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 5) link_NAG-ASN : angle 4.10436 ( 15) hydrogen bonds : bond 0.04167 ( 562) hydrogen bonds : angle 7.78897 ( 1476) SS BOND : bond 0.00283 ( 26) SS BOND : angle 1.24491 ( 52) covalent geometry : bond 0.00315 (17537) covalent geometry : angle 0.63150 (23896) *********************** 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 : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 TYR cc_start: 0.8738 (m-80) cc_final: 0.8266 (m-80) REVERT: R 264 MET cc_start: 0.8602 (mmp) cc_final: 0.8310 (mmt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2506 time to fit residues: 41.0435 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 : 1.896 ------------------------------------------------------------------------------- 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: 0.0670 chunk 198 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 213 optimal weight: 0.2980 chunk 220 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3094 ASN ** 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.046506 restraints weight = 158305.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046807 restraints weight = 116263.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.046907 restraints weight = 79761.938| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17568 Z= 0.118 Angle : 0.618 11.059 23963 Z= 0.312 Chirality : 0.044 0.452 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.162 55.133 2519 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -2.20 (0.18), residues: 2272 helix: -0.62 (0.28), residues: 339 sheet: -1.82 (0.17), residues: 871 loop : -1.25 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 165 HIS 0.007 0.001 HIS A1944 PHE 0.016 0.001 PHE A2057 TYR 0.018 0.001 TYR A3074 ARG 0.005 0.000 ARG A3092 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 5) link_NAG-ASN : angle 3.86721 ( 15) hydrogen bonds : bond 0.03395 ( 562) hydrogen bonds : angle 7.03628 ( 1476) SS BOND : bond 0.00256 ( 26) SS BOND : angle 1.07563 ( 52) covalent geometry : bond 0.00249 (17537) covalent geometry : angle 0.60915 (23896) *********************** 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 96 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3007 MET cc_start: 0.9468 (tmm) cc_final: 0.9253 (tmm) REVERT: A 3438 MET cc_start: 0.8765 (tmm) cc_final: 0.8529 (tmm) REVERT: B 342 TYR cc_start: 0.8429 (m-80) cc_final: 0.8106 (m-80) REVERT: R 264 MET cc_start: 0.8493 (mmp) cc_final: 0.8065 (mmt) REVERT: R 298 MET cc_start: 0.7386 (mpp) cc_final: 0.7057 (mpp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3424 time to fit residues: 57.2786 Evaluate side-chains 77 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.960 ------------------------------------------------------------------------------- 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: 0.9980 chunk 163 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** A2982 ASN ** 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** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.057278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043613 restraints weight = 158791.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044526 restraints weight = 96646.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.045129 restraints weight = 69791.572| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17568 Z= 0.236 Angle : 0.678 10.639 23963 Z= 0.350 Chirality : 0.044 0.472 2792 Planarity : 0.004 0.052 3118 Dihedral : 5.510 53.481 2519 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % 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: -2.26 (0.18), residues: 2272 helix: -0.47 (0.29), residues: 329 sheet: -1.96 (0.17), residues: 872 loop : -1.25 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A3633 HIS 0.007 0.002 HIS A3114 PHE 0.021 0.002 PHE A3343 TYR 0.020 0.002 TYR H 95 ARG 0.009 0.001 ARG A2012 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 5) link_NAG-ASN : angle 3.87230 ( 15) hydrogen bonds : bond 0.03759 ( 562) hydrogen bonds : angle 7.13498 ( 1476) SS BOND : bond 0.00624 ( 26) SS BOND : angle 1.43125 ( 52) covalent geometry : bond 0.00501 (17537) covalent geometry : angle 0.66907 (23896) *********************** 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 91 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9393 (mmm) cc_final: 0.9135 (mmm) REVERT: A 1900 MET cc_start: 0.9137 (mpp) cc_final: 0.8929 (mpp) REVERT: A 3007 MET cc_start: 0.9490 (tmm) cc_final: 0.9241 (tmm) REVERT: A 3438 MET cc_start: 0.8995 (tmm) cc_final: 0.8757 (tmm) REVERT: B 342 TYR cc_start: 0.8733 (m-80) cc_final: 0.8312 (m-80) REVERT: R 264 MET cc_start: 0.8642 (mmp) cc_final: 0.8330 (mmt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2963 time to fit residues: 45.3305 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 : 2.102 ------------------------------------------------------------------------------- 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: 3.9990 chunk 115 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 366 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.058202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046716 restraints weight = 161267.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046731 restraints weight = 99117.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046702 restraints weight = 86704.847| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17568 Z= 0.121 Angle : 0.617 10.944 23963 Z= 0.310 Chirality : 0.044 0.435 2792 Planarity : 0.004 0.060 3118 Dihedral : 5.184 54.592 2519 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % 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: -0.51 (0.28), residues: 347 sheet: -1.86 (0.17), residues: 872 loop : -1.24 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 165 HIS 0.004 0.001 HIS A1944 PHE 0.017 0.001 PHE A2057 TYR 0.021 0.001 TYR A3074 ARG 0.004 0.000 ARG A3092 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 5) link_NAG-ASN : angle 3.81849 ( 15) hydrogen bonds : bond 0.03150 ( 562) hydrogen bonds : angle 6.66298 ( 1476) SS BOND : bond 0.00296 ( 26) SS BOND : angle 1.33934 ( 52) covalent geometry : bond 0.00258 (17537) covalent geometry : angle 0.60679 (23896) *********************** 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 97 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9371 (mmm) cc_final: 0.9058 (mmm) REVERT: A 3007 MET cc_start: 0.9366 (tmm) cc_final: 0.9075 (tmm) REVERT: B 333 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7702 (p0) REVERT: B 342 TYR cc_start: 0.8529 (m-80) cc_final: 0.8254 (m-80) REVERT: R 264 MET cc_start: 0.8528 (mmp) cc_final: 0.8089 (mmt) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.3741 time to fit residues: 64.1505 Evaluate side-chains 72 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 4.319 ------------------------------------------------------------------------------- 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: 9.9990 chunk 169 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 148 optimal weight: 0.0040 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 199 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 overall best weight: 0.7752 ------------------------------------------------------------------------------- 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** ** A3606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.058693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.045148 restraints weight = 155747.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.046074 restraints weight = 95430.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.046685 restraints weight = 68899.557| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17568 Z= 0.130 Angle : 0.616 10.999 23963 Z= 0.312 Chirality : 0.044 0.451 2792 Planarity : 0.004 0.051 3118 Dihedral : 5.124 54.866 2519 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.15 (0.18), residues: 2272 helix: -0.43 (0.28), residues: 348 sheet: -1.83 (0.17), residues: 863 loop : -1.24 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 165 HIS 0.015 0.001 HIS A3410 PHE 0.017 0.001 PHE A2057 TYR 0.020 0.001 TYR A3074 ARG 0.003 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 5) link_NAG-ASN : angle 4.99453 ( 15) hydrogen bonds : bond 0.03131 ( 562) hydrogen bonds : angle 6.57055 ( 1476) SS BOND : bond 0.00253 ( 26) SS BOND : angle 1.18755 ( 52) covalent geometry : bond 0.00280 (17537) covalent geometry : angle 0.60161 (23896) *********************** 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 93 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9435 (mmm) cc_final: 0.9070 (mmm) REVERT: A 3007 MET cc_start: 0.9340 (tmm) cc_final: 0.9064 (tmm) REVERT: B 342 TYR cc_start: 0.8841 (m-80) cc_final: 0.8399 (m-80) REVERT: R 264 MET cc_start: 0.8573 (mmp) cc_final: 0.8256 (mmt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2502 time to fit residues: 40.1694 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 : 1.851 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 4.9990 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: 7.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 146 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.056891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043096 restraints weight = 160195.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.044000 restraints weight = 97654.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.044585 restraints weight = 70563.506| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 17568 Z= 0.277 Angle : 0.724 11.690 23963 Z= 0.373 Chirality : 0.045 0.469 2792 Planarity : 0.005 0.053 3118 Dihedral : 5.683 52.970 2519 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -2.35 (0.18), residues: 2272 helix: -0.53 (0.28), residues: 339 sheet: -2.03 (0.17), residues: 877 loop : -1.30 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A3633 HIS 0.013 0.002 HIS R 285 PHE 0.028 0.002 PHE A3343 TYR 0.024 0.002 TYR A3520 ARG 0.005 0.001 ARG N 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 5) link_NAG-ASN : angle 4.49808 ( 15) hydrogen bonds : bond 0.03785 ( 562) hydrogen bonds : angle 6.97703 ( 1476) SS BOND : bond 0.00454 ( 26) SS BOND : angle 1.51349 ( 52) covalent geometry : bond 0.00586 (17537) covalent geometry : angle 0.71238 (23896) *********************** 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 91 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1881 MET cc_start: 0.9470 (mmm) cc_final: 0.9081 (mmm) REVERT: A 3007 MET cc_start: 0.9363 (tmm) cc_final: 0.9065 (tmm) REVERT: B 342 TYR cc_start: 0.8794 (m-80) cc_final: 0.8365 (m-80) REVERT: B 424 PHE cc_start: 0.8411 (m-80) cc_final: 0.8202 (m-80) REVERT: R 264 MET cc_start: 0.8660 (mmp) cc_final: 0.8339 (mmt) REVERT: R 298 MET cc_start: 0.7669 (mpp) cc_final: 0.7374 (mpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2484 time to fit residues: 38.2890 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 : 1.828 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.3671 r_free = 0.3671 target = 0.058487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.044720 restraints weight = 156099.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.045681 restraints weight = 93612.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046308 restraints weight = 66920.938| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17568 Z= 0.130 Angle : 0.646 11.239 23963 Z= 0.324 Chirality : 0.045 0.440 2792 Planarity : 0.004 0.053 3118 Dihedral : 5.346 54.191 2519 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.21 (0.18), residues: 2272 helix: -0.50 (0.28), residues: 350 sheet: -1.93 (0.17), residues: 872 loop : -1.20 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 165 HIS 0.014 0.001 HIS A3410 PHE 0.017 0.001 PHE A2057 TYR 0.026 0.001 TYR A3074 ARG 0.003 0.000 ARG A3527 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 5) link_NAG-ASN : angle 4.42320 ( 15) hydrogen bonds : bond 0.03130 ( 562) hydrogen bonds : angle 6.63021 ( 1476) SS BOND : bond 0.00274 ( 26) SS BOND : angle 1.22861 ( 52) covalent geometry : bond 0.00279 (17537) covalent geometry : angle 0.63510 (23896) *********************** 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 93 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3007 MET cc_start: 0.9327 (tmm) cc_final: 0.8982 (tmm) REVERT: B 342 TYR cc_start: 0.8773 (m-80) cc_final: 0.8343 (m-80) REVERT: R 264 MET cc_start: 0.8624 (mmp) cc_final: 0.8273 (mmt) REVERT: R 298 MET cc_start: 0.7393 (mpp) cc_final: 0.7153 (mpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3361 time to fit residues: 54.6293 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 : 2.170 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** A3176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3583 HIS ** 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 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 = 0.3632 r_free = 0.3632 target = 0.057140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043260 restraints weight = 159145.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044173 restraints weight = 97167.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.044766 restraints weight = 70175.120| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17568 Z= 0.244 Angle : 0.704 11.455 23963 Z= 0.361 Chirality : 0.045 0.458 2792 Planarity : 0.004 0.057 3118 Dihedral : 5.673 53.380 2519 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -2.40 (0.18), residues: 2272 helix: -0.65 (0.28), residues: 345 sheet: -2.07 (0.17), residues: 878 loop : -1.29 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A3633 HIS 0.009 0.002 HIS R 285 PHE 0.023 0.002 PHE A3343 TYR 0.022 0.002 TYR A3520 ARG 0.005 0.001 ARG N 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 5) link_NAG-ASN : angle 4.31671 ( 15) hydrogen bonds : bond 0.03583 ( 562) hydrogen bonds : angle 6.90391 ( 1476) SS BOND : bond 0.00349 ( 26) SS BOND : angle 1.32706 ( 52) covalent geometry : bond 0.00521 (17537) covalent geometry : angle 0.69404 (23896) ********************** 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 89 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3007 MET cc_start: 0.9369 (tmm) cc_final: 0.8983 (tmm) REVERT: B 342 TYR cc_start: 0.8849 (m-80) cc_final: 0.8421 (m-80) REVERT: R 264 MET cc_start: 0.8667 (mmp) cc_final: 0.8326 (mmt) REVERT: R 298 MET cc_start: 0.7661 (mpp) cc_final: 0.7368 (mpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4064 time to fit residues: 63.6265 Evaluate side-chains 70 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.702 ------------------------------------------------------------------------------- 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: 1.9990 chunk 192 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 228 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.058323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.044564 restraints weight = 155720.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.045503 restraints weight = 94329.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046118 restraints weight = 68016.920| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17568 Z= 0.137 Angle : 0.646 11.172 23963 Z= 0.324 Chirality : 0.045 0.428 2792 Planarity : 0.004 0.055 3118 Dihedral : 5.362 54.378 2519 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.62 (0.28), residues: 358 sheet: -1.95 (0.17), residues: 874 loop : -1.21 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 165 HIS 0.011 0.001 HIS A3410 PHE 0.019 0.001 PHE B 259 TYR 0.018 0.001 TYR A3177 ARG 0.003 0.000 ARG A2444 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 5) link_NAG-ASN : angle 4.29902 ( 15) hydrogen bonds : bond 0.03096 ( 562) hydrogen bonds : angle 6.61541 ( 1476) SS BOND : bond 0.00274 ( 26) SS BOND : angle 1.14762 ( 52) covalent geometry : bond 0.00296 (17537) covalent geometry : angle 0.63598 (23896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6999.66 seconds wall clock time: 125 minutes 56.51 seconds (7556.51 seconds total)