Starting phenix.real_space_refine on Sat Mar 16 07:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bo2_16138/03_2024/8bo2_16138.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 8835 2.51 5 N 2399 2.21 5 O 2762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14037 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6229 Classifications: {'peptide': 787} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 356 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "P" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2335 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Time building chain proxies: 7.24, per 1000 atoms: 0.52 Number of scatterers: 14037 At special positions: 0 Unit cell: (104.16, 138.57, 140.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2762 8.00 N 2399 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.01 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 21.0% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.620A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.811A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.605A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.906A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.528A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.600A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.791A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.224A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.011A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.577A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.751A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.822A pdb=" N ASP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.758A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.928A pdb=" N SER D 133 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.550A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.700A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.907A pdb=" N ILE D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.530A pdb=" N VAL E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'P' and resid 1000 through 1024 removed outlier: 4.002A pdb=" N ASP P1014 " --> pdb=" O LEU P1010 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR P1015 " --> pdb=" O PHE P1011 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN P1024 " --> pdb=" O ASN P1020 " (cutoff:3.500A) Processing helix chain 'P' and resid 1025 through 1035 removed outlier: 3.682A pdb=" N ASP P1031 " --> pdb=" O LYS P1027 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU P1032 " --> pdb=" O ARG P1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.235A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 83 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.286A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.805A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.936A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 337 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 274 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.258A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.903A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.131A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.529A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 4.102A pdb=" N ALA B 218 " --> pdb=" O TRP B 228 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.969A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.606A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AB8, first strand: chain 'P' and resid 1159 through 1162 removed outlier: 4.545A pdb=" N VAL P1161 " --> pdb=" O ALA P1165 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET P1258 " --> pdb=" O ALA P1282 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA P1282 " --> pdb=" O MET P1258 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET P1260 " --> pdb=" O LYS P1280 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS P1280 " --> pdb=" O MET P1260 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL P1262 " --> pdb=" O PHE P1278 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG P1273 " --> pdb=" O ARG P1297 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG P1297 " --> pdb=" O ARG P1273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY P1275 " --> pdb=" O ASN P1295 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU P1277 " --> pdb=" O ASN P1293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P1291 " --> pdb=" O GLU P1279 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER P1281 " --> pdb=" O ASP P1289 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP P1289 " --> pdb=" O SER P1281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL P1288 " --> pdb=" O SER P1051 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER P1051 " --> pdb=" O VAL P1288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU P1078 " --> pdb=" O HIS P1071 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 1182 through 1187 696 hydrogen bonds defined for protein. 1944 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: 5.32 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3004 1.33 - 1.46: 5120 1.46 - 1.58: 6139 1.58 - 1.71: 2 1.71 - 1.83: 78 Bond restraints: 14343 Sorted by residual: bond pdb=" CA ARG B 195 " pdb=" C ARG B 195 " ideal model delta sigma weight residual 1.532 1.493 0.039 9.60e-03 1.09e+04 1.69e+01 bond pdb=" ND1 HIS B 324 " pdb=" CE1 HIS B 324 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" ND1 HIS C 51 " pdb=" CE1 HIS C 51 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+01 bond pdb=" ND1 HIS E 83 " pdb=" CE1 HIS E 83 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CD ARG B 195 " pdb=" NE ARG B 195 " ideal model delta sigma weight residual 1.458 1.514 -0.056 1.40e-02 5.10e+03 1.59e+01 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 88.66 - 97.76: 23 97.76 - 106.85: 513 106.85 - 115.94: 8183 115.94 - 125.04: 10280 125.04 - 134.13: 475 Bond angle restraints: 19474 Sorted by residual: angle pdb=" CA ASP A 683 " pdb=" CB ASP A 683 " pdb=" CG ASP A 683 " ideal model delta sigma weight residual 112.60 104.35 8.25 1.00e+00 1.00e+00 6.81e+01 angle pdb=" CA ASP D 146 " pdb=" CB ASP D 146 " pdb=" CG ASP D 146 " ideal model delta sigma weight residual 112.60 104.81 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" CA ASP D 131 " pdb=" CB ASP D 131 " pdb=" CG ASP D 131 " ideal model delta sigma weight residual 112.60 105.02 7.58 1.00e+00 1.00e+00 5.74e+01 angle pdb=" CA ASP A 762 " pdb=" CB ASP A 762 " pdb=" CG ASP A 762 " ideal model delta sigma weight residual 112.60 118.76 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA ASP A 694 " pdb=" CB ASP A 694 " pdb=" CG ASP A 694 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 ... (remaining 19469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7722 17.59 - 35.18: 555 35.18 - 52.77: 95 52.77 - 70.37: 45 70.37 - 87.96: 21 Dihedral angle restraints: 8438 sinusoidal: 3274 harmonic: 5164 Sorted by residual: dihedral pdb=" CA VAL A 543 " pdb=" C VAL A 543 " pdb=" N ALA A 544 " pdb=" CA ALA A 544 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" C ASP A 795 " pdb=" N ASP A 795 " pdb=" CA ASP A 795 " pdb=" CB ASP A 795 " ideal model delta harmonic sigma weight residual -122.60 -135.79 13.19 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1413 0.097 - 0.195: 550 0.195 - 0.292: 113 0.292 - 0.389: 24 0.389 - 0.487: 8 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA ASP A 795 " pdb=" N ASP A 795 " pdb=" C ASP A 795 " pdb=" CB ASP A 795 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA ASP B 159 " pdb=" N ASP B 159 " pdb=" C ASP B 159 " pdb=" CB ASP B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 2105 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P1298 " 0.245 2.00e-02 2.50e+03 1.44e-01 4.16e+02 pdb=" CG TYR P1298 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR P1298 " -0.157 2.00e-02 2.50e+03 pdb=" CD2 TYR P1298 " -0.106 2.00e-02 2.50e+03 pdb=" CE1 TYR P1298 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR P1298 " -0.131 2.00e-02 2.50e+03 pdb=" CZ TYR P1298 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR P1298 " 0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " 0.144 2.00e-02 2.50e+03 1.10e-01 2.40e+02 pdb=" CG TYR A 230 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " -0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 222 " 0.130 2.00e-02 2.50e+03 7.55e-02 1.14e+02 pdb=" CG TYR D 222 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 222 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR D 222 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR D 222 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR D 222 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR D 222 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR D 222 " 0.129 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6880 2.98 - 3.46: 14041 3.46 - 3.94: 23547 3.94 - 4.42: 26197 4.42 - 4.90: 43793 Nonbonded interactions: 114458 Sorted by model distance: nonbonded pdb=" OD2 ASP P1232 " pdb=" NZ LYS P1254 " model vdw 2.505 2.520 nonbonded pdb=" OH TYR P1118 " pdb=" OE1 GLU P1154 " model vdw 2.507 2.440 nonbonded pdb=" OH TYR A 468 " pdb=" OE1 GLU A 470 " model vdw 2.534 2.440 nonbonded pdb=" O LEU B 110 " pdb=" N GLU B 127 " model vdw 2.535 2.520 nonbonded pdb=" NZ LYS A 106 " pdb=" OE1 GLU P1072 " model vdw 2.541 2.520 ... (remaining 114453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.320 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.500 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5137 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 : 0.017 0.057 14343 Z= 1.091 Angle : 1.935 12.238 19474 Z= 1.344 Chirality : 0.108 0.487 2108 Planarity : 0.015 0.157 2566 Dihedral : 14.135 87.956 5156 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 0.47 % Allowed : 4.37 % Favored : 95.16 % Cbeta Deviations : 0.61 % 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: -0.67 (0.19), residues: 1791 helix: 0.84 (0.28), residues: 343 sheet: 0.35 (0.20), residues: 641 loop : -1.72 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.021 TRP B 228 HIS 0.017 0.005 HIS B 64 PHE 0.082 0.014 PHE D 144 TYR 0.245 0.024 TYR P1298 ARG 0.006 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.4842 (mmm) cc_final: 0.4214 (mmp) REVERT: D 109 MET cc_start: 0.4884 (mtp) cc_final: 0.4522 (mtp) outliers start: 7 outliers final: 3 residues processed: 238 average time/residue: 0.2794 time to fit residues: 97.3757 Evaluate side-chains 168 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain P residue 1045 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 ASN A 207 ASN A 239 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 168 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 104 ASN D 116 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN P1064 GLN P1071 HIS P1128 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14343 Z= 0.283 Angle : 0.622 7.124 19474 Z= 0.334 Chirality : 0.045 0.155 2108 Planarity : 0.004 0.044 2566 Dihedral : 5.547 53.651 1981 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 1.88 % Allowed : 9.41 % Favored : 88.70 % 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: -0.56 (0.19), residues: 1791 helix: 0.80 (0.28), residues: 358 sheet: 0.37 (0.20), residues: 636 loop : -1.55 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 810 HIS 0.006 0.001 HIS B 324 PHE 0.015 0.002 PHE A 565 TYR 0.021 0.002 TYR P1060 ARG 0.007 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.4487 (mmm) cc_final: 0.4092 (mmp) REVERT: D 207 ASP cc_start: 0.5283 (OUTLIER) cc_final: 0.5016 (m-30) REVERT: P 1194 MET cc_start: 0.2217 (ppp) cc_final: 0.1818 (ppp) outliers start: 28 outliers final: 17 residues processed: 207 average time/residue: 0.2357 time to fit residues: 74.5140 Evaluate side-chains 178 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 40.0000 chunk 174 optimal weight: 30.0000 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.0570 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 334 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1071 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 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 : 0.004 0.057 14343 Z= 0.224 Angle : 0.583 8.002 19474 Z= 0.311 Chirality : 0.044 0.165 2108 Planarity : 0.004 0.040 2566 Dihedral : 5.249 57.890 1977 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.19 % Rotamer: Outliers : 2.22 % Allowed : 11.57 % Favored : 86.21 % 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: -0.58 (0.20), residues: 1791 helix: 0.81 (0.28), residues: 357 sheet: 0.32 (0.20), residues: 626 loop : -1.52 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 810 HIS 0.005 0.001 HIS B 324 PHE 0.022 0.001 PHE P1082 TYR 0.031 0.001 TYR A 255 ARG 0.005 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.2708 (OUTLIER) cc_final: 0.2489 (mm) REVERT: D 207 ASP cc_start: 0.5157 (OUTLIER) cc_final: 0.4896 (m-30) outliers start: 33 outliers final: 24 residues processed: 200 average time/residue: 0.2392 time to fit residues: 72.1662 Evaluate side-chains 188 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 0.0670 chunk 17 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 40.0000 chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 334 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 14343 Z= 0.451 Angle : 0.699 7.392 19474 Z= 0.376 Chirality : 0.047 0.257 2108 Planarity : 0.005 0.061 2566 Dihedral : 5.664 51.115 1977 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 3.63 % Allowed : 13.25 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1791 helix: 0.47 (0.27), residues: 356 sheet: 0.05 (0.20), residues: 622 loop : -1.71 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P1042 HIS 0.006 0.001 HIS B 324 PHE 0.019 0.002 PHE D 128 TYR 0.033 0.002 TYR B 333 ARG 0.006 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 170 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 207 ASP cc_start: 0.5471 (OUTLIER) cc_final: 0.5256 (m-30) REVERT: P 1194 MET cc_start: 0.2174 (ppp) cc_final: 0.1656 (ppp) outliers start: 54 outliers final: 40 residues processed: 208 average time/residue: 0.2324 time to fit residues: 74.3159 Evaluate side-chains 186 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1035 ILE Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1174 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 128 optimal weight: 0.0870 chunk 70 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 87 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN B 168 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14343 Z= 0.154 Angle : 0.580 9.362 19474 Z= 0.305 Chirality : 0.044 0.162 2108 Planarity : 0.003 0.036 2566 Dihedral : 5.119 53.998 1977 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 2.35 % Allowed : 15.33 % Favored : 82.31 % 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: -0.67 (0.20), residues: 1791 helix: 0.86 (0.28), residues: 357 sheet: 0.20 (0.21), residues: 623 loop : -1.57 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.004 0.001 HIS B 324 PHE 0.021 0.001 PHE A 426 TYR 0.025 0.001 TYR B 333 ARG 0.005 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1194 MET cc_start: 0.2136 (ppp) cc_final: 0.1606 (ppp) outliers start: 35 outliers final: 24 residues processed: 203 average time/residue: 0.2299 time to fit residues: 70.5872 Evaluate side-chains 176 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1174 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 166 optimal weight: 50.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 215 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14343 Z= 0.301 Angle : 0.628 7.886 19474 Z= 0.332 Chirality : 0.045 0.189 2108 Planarity : 0.004 0.067 2566 Dihedral : 5.163 50.559 1977 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.25 % Favored : 93.58 % Rotamer: Outliers : 2.69 % Allowed : 16.68 % Favored : 80.63 % 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: -0.73 (0.20), residues: 1791 helix: 0.80 (0.28), residues: 356 sheet: 0.13 (0.21), residues: 621 loop : -1.57 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 PHE 0.020 0.002 PHE A 426 TYR 0.023 0.002 TYR A 255 ARG 0.006 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1194 MET cc_start: 0.2268 (ppp) cc_final: 0.1743 (ppp) outliers start: 40 outliers final: 32 residues processed: 190 average time/residue: 0.2469 time to fit residues: 71.0188 Evaluate side-chains 182 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain P residue 1035 ILE Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1174 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14343 Z= 0.287 Angle : 0.618 8.466 19474 Z= 0.325 Chirality : 0.045 0.184 2108 Planarity : 0.004 0.033 2566 Dihedral : 5.182 51.300 1977 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 2.69 % Allowed : 17.55 % Favored : 79.76 % 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: -0.76 (0.20), residues: 1791 helix: 0.80 (0.28), residues: 356 sheet: 0.03 (0.20), residues: 636 loop : -1.56 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 PHE 0.027 0.002 PHE A 738 TYR 0.023 0.002 TYR B 333 ARG 0.007 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: P 1194 MET cc_start: 0.2348 (ppp) cc_final: 0.1934 (ppp) outliers start: 40 outliers final: 32 residues processed: 185 average time/residue: 0.2464 time to fit residues: 68.6246 Evaluate side-chains 182 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1035 ILE Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 170 GLN B 186 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14343 Z= 0.198 Angle : 0.597 10.841 19474 Z= 0.312 Chirality : 0.044 0.167 2108 Planarity : 0.003 0.033 2566 Dihedral : 5.048 52.078 1977 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 2.42 % Allowed : 18.43 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1791 helix: 0.95 (0.29), residues: 356 sheet: 0.07 (0.20), residues: 638 loop : -1.51 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.003 0.001 HIS B 324 PHE 0.021 0.001 PHE A 197 TYR 0.022 0.001 TYR B 333 ARG 0.006 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1194 MET cc_start: 0.2328 (ppp) cc_final: 0.1997 (ppp) outliers start: 36 outliers final: 28 residues processed: 187 average time/residue: 0.2367 time to fit residues: 66.5516 Evaluate side-chains 183 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 5.9990 chunk 159 optimal weight: 0.0000 chunk 164 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14343 Z= 0.202 Angle : 0.612 11.112 19474 Z= 0.317 Chirality : 0.044 0.170 2108 Planarity : 0.004 0.059 2566 Dihedral : 4.971 51.714 1977 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.97 % Rotamer: Outliers : 2.15 % Allowed : 18.56 % Favored : 79.29 % 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: -0.63 (0.20), residues: 1791 helix: 0.99 (0.29), residues: 355 sheet: 0.09 (0.20), residues: 638 loop : -1.49 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 PHE 0.019 0.001 PHE A 426 TYR 0.022 0.001 TYR B 333 ARG 0.007 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1194 MET cc_start: 0.2316 (ppp) cc_final: 0.1980 (ppp) outliers start: 32 outliers final: 27 residues processed: 182 average time/residue: 0.2152 time to fit residues: 60.4860 Evaluate side-chains 175 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1035 ILE Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 0.0040 chunk 86 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5339 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14343 Z= 0.175 Angle : 0.617 12.136 19474 Z= 0.317 Chirality : 0.044 0.159 2108 Planarity : 0.004 0.048 2566 Dihedral : 4.870 52.332 1977 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 1.82 % Allowed : 18.76 % Favored : 79.42 % 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: -0.56 (0.20), residues: 1791 helix: 1.11 (0.29), residues: 356 sheet: 0.16 (0.21), residues: 631 loop : -1.50 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 PHE 0.018 0.001 PHE A 426 TYR 0.022 0.001 TYR B 333 ARG 0.006 0.000 ARG D 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1194 MET cc_start: 0.2236 (ppp) cc_final: 0.1915 (ppp) outliers start: 27 outliers final: 24 residues processed: 185 average time/residue: 0.2399 time to fit residues: 68.2894 Evaluate side-chains 183 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094101 restraints weight = 32198.778| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.06 r_work: 0.3423 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14343 Z= 0.201 Angle : 0.634 11.961 19474 Z= 0.326 Chirality : 0.044 0.160 2108 Planarity : 0.004 0.049 2566 Dihedral : 4.883 51.872 1977 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.15 % Allowed : 18.63 % Favored : 79.22 % 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: -0.58 (0.20), residues: 1791 helix: 1.06 (0.29), residues: 356 sheet: 0.14 (0.21), residues: 632 loop : -1.50 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.004 0.001 HIS P1086 PHE 0.019 0.001 PHE A 426 TYR 0.022 0.001 TYR B 333 ARG 0.008 0.000 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3315.33 seconds wall clock time: 60 minutes 23.31 seconds (3623.31 seconds total)