Starting phenix.real_space_refine on Sun Dec 10 03:16:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yov_33988/12_2023/7yov_33988.pdb" } resolution = 3.25 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= 0.003 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 82 5.16 5 C 8368 2.51 5 N 2307 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 241": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1077": "NH1" <-> "NH2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A ARG 1093": "NH1" <-> "NH2" Residue "A ARG 1101": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ARG 1189": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13232 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} bond proxies already assigned to first conformer: 570 Chain: "C" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 537 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1186 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 12, 'TRANS': 145} Chain breaks: 1 Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 516 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "A" Number of atoms: 10416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 10416 Classifications: {'peptide': 1310} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1252} Chain breaks: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA D 301 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 301 " occ=0.50 Time building chain proxies: 7.16, per 1000 atoms: 0.54 Number of scatterers: 13232 At special positions: 0 Unit cell: (106.08, 159.12, 109.2, 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 82 16.00 O 2475 8.00 N 2307 7.00 C 8368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1350 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1160 " distance=2.03 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: 5.28 Conformation dependent library (CDL) restraints added in 2.7 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 6 sheets defined 57.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'D' and resid 238 through 280 removed outlier: 4.277A pdb=" N ASP D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 252 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Proline residue: D 260 - end of helix removed outlier: 3.574A pdb=" N THR D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 Processing helix chain 'C' and resid 237 through 285 removed outlier: 3.984A pdb=" N THR C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Proline residue: C 260 - end of helix removed outlier: 4.227A pdb=" N VAL C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'E' and resid 237 through 278 removed outlier: 3.994A pdb=" N SER E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Proline residue: E 260 - end of helix removed outlier: 3.867A pdb=" N SER E 264 " --> pdb=" O PRO E 260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET E 276 " --> pdb=" O SER E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.581A pdb=" N VAL E 320 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.534A pdb=" N ASP E 340 " --> pdb=" O HIS E 337 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 341' Processing helix chain 'E' and resid 352 through 366 Processing helix chain 'E' and resid 369 through 382 removed outlier: 3.602A pdb=" N LEU E 380 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 382 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 397 removed outlier: 3.522A pdb=" N ILE E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 274 removed outlier: 3.921A pdb=" N ILE B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Proline residue: B 260 - end of helix removed outlier: 3.593A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.916A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.724A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.855A pdb=" N ARG A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.672A pdb=" N GLY A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 141 removed outlier: 4.120A pdb=" N ILE A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.531A pdb=" N CYS A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.717A pdb=" N ALA A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 removed outlier: 3.709A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.728A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.907A pdb=" N VAL A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.518A pdb=" N PHE A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.557A pdb=" N SER A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.518A pdb=" N LEU A 356 " --> pdb=" O MET A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.059A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 removed outlier: 3.619A pdb=" N GLN A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.522A pdb=" N PHE A 484 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.581A pdb=" N LYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.704A pdb=" N PHE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.714A pdb=" N GLU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.869A pdb=" N SER A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 removed outlier: 5.374A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.804A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.714A pdb=" N TRP A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 removed outlier: 3.832A pdb=" N HIS A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 830 removed outlier: 3.746A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.708A pdb=" N SER A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.604A pdb=" N TYR A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 883 " --> pdb=" O TYR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 4.004A pdb=" N SER A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 933 through 948 removed outlier: 3.757A pdb=" N THR A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 4.096A pdb=" N MET A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 986 through 1000 removed outlier: 3.530A pdb=" N PHE A1000 " --> pdb=" O GLN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.763A pdb=" N GLU A1020 " --> pdb=" O ASN A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 removed outlier: 3.672A pdb=" N ALA A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1055 Processing helix chain 'A' and resid 1060 through 1070 removed outlier: 3.840A pdb=" N ILE A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1083 Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1112 through 1125 removed outlier: 3.718A pdb=" N LEU A1116 " --> pdb=" O CYS A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.820A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1230 Processing helix chain 'A' and resid 1232 through 1245 removed outlier: 3.575A pdb=" N ALA A1238 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A1245 " --> pdb=" O LYS A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 4.098A pdb=" N LEU A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 4.161A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1328 removed outlier: 3.704A pdb=" N LEU A1318 " --> pdb=" O GLN A1314 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A1325 " --> pdb=" O LEU A1321 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A1328 " --> pdb=" O ILE A1324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310 removed outlier: 3.502A pdb=" N VAL A 384 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 382 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.648A pdb=" N GLN A 208 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 744 removed outlier: 4.367A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 807 through 810 Processing sheet with id=AA6, first strand: chain 'A' and resid 1292 through 1294 614 hydrogen bonds defined for protein. 1765 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: 4.22 Time building geometry restraints manager: 5.72 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: 3968 1.33 - 1.45: 2289 1.45 - 1.57: 7089 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 13480 Sorted by residual: bond pdb=" C ILE E 259 " pdb=" N PRO E 260 " ideal model delta sigma weight residual 1.336 1.394 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" C ALA A 474 " pdb=" N HIS A 475 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.47e-02 4.63e+03 1.23e+01 bond pdb=" CB VAL A 748 " pdb=" CG1 VAL A 748 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CG LEU A 647 " pdb=" CD1 LEU A 647 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" CB MET D 276 " pdb=" CG MET D 276 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.12e+00 ... (remaining 13475 not shown) Histogram of bond angle deviations from ideal: 94.95 - 102.78: 90 102.78 - 110.60: 4215 110.60 - 118.43: 6463 118.43 - 126.26: 7274 126.26 - 134.08: 208 Bond angle restraints: 18250 Sorted by residual: angle pdb=" CA LEU A1008 " pdb=" CB LEU A1008 " pdb=" CG LEU A1008 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.50e+01 angle pdb=" C GLY E 314 " pdb=" N ASP E 315 " pdb=" CA ASP E 315 " ideal model delta sigma weight residual 121.61 128.48 -6.87 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C PHE A 580 " pdb=" N GLN A 581 " pdb=" CA GLN A 581 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" CA LEU E 286 " pdb=" CB LEU E 286 " pdb=" CG LEU E 286 " ideal model delta sigma weight residual 116.30 131.51 -15.21 3.50e+00 8.16e-02 1.89e+01 ... (remaining 18245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 7701 15.42 - 30.83: 449 30.83 - 46.24: 103 46.24 - 61.66: 13 61.66 - 77.07: 14 Dihedral angle restraints: 8280 sinusoidal: 3335 harmonic: 4945 Sorted by residual: dihedral pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual 93.00 157.59 -64.59 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA SER A1283 " pdb=" C SER A1283 " pdb=" N LEU A1284 " pdb=" CA LEU A1284 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASN A 795 " pdb=" C ASN A 795 " pdb=" N LEU A 796 " pdb=" CA LEU A 796 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1611 0.068 - 0.137: 437 0.137 - 0.205: 58 0.205 - 0.273: 10 0.273 - 0.342: 2 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE A 674 " pdb=" CA ILE A 674 " pdb=" CG1 ILE A 674 " pdb=" CG2 ILE A 674 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE D 238 " pdb=" CA ILE D 238 " pdb=" CG1 ILE D 238 " pdb=" CG2 ILE D 238 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2115 not shown) Planarity restraints: 2323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.024 2.00e-02 2.50e+03 2.80e-02 1.38e+01 pdb=" CG PHE A 395 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " 0.017 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A 33 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 412 " 0.019 2.00e-02 2.50e+03 1.98e-02 9.76e+00 pdb=" CG TRP A 412 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 412 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 412 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 412 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 412 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 412 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 412 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 412 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 412 " 0.001 2.00e-02 2.50e+03 ... (remaining 2320 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 240 2.66 - 3.22: 12386 3.22 - 3.78: 20834 3.78 - 4.34: 28551 4.34 - 4.90: 47088 Nonbonded interactions: 109099 Sorted by model distance: nonbonded pdb=" NE2 GLN E 255 " pdb=" OD1 ASP B 250 " model vdw 2.102 2.520 nonbonded pdb=" NH1 ARG E 263 " pdb=" OG1 THR B 261 " model vdw 2.214 2.520 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASP A 245 " model vdw 2.236 2.440 nonbonded pdb=" O GLU A 840 " pdb=" OG SER A1085 " model vdw 2.270 2.440 nonbonded pdb=" O ASP A1094 " pdb=" OG SER A1099 " model vdw 2.279 2.440 ... (remaining 109094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 236 through 300) selection = (chain 'C' and resid 236 through 300) selection = (chain 'D' and resid 236 through 300) } 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=0.50 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.530 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 37.300 Find NCS groups from input model: 0.410 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.011 0.103 13480 Z= 0.728 Angle : 1.167 17.484 18250 Z= 0.615 Chirality : 0.063 0.342 2118 Planarity : 0.009 0.077 2323 Dihedral : 11.203 77.075 5046 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.14 % Allowed : 3.28 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -3.95 (0.16), residues: 1660 helix: -2.73 (0.12), residues: 884 sheet: -0.72 (0.64), residues: 71 loop : -2.53 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP A 33 HIS 0.015 0.003 HIS A 475 PHE 0.061 0.005 PHE A 395 TYR 0.038 0.004 TYR A 908 ARG 0.015 0.002 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 356 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 369 average time/residue: 0.3416 time to fit residues: 169.2515 Evaluate side-chains 204 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1145 time to fit residues: 2.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN C 248 GLN E 279 ASN E 369 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 248 ASN A 316 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN A 575 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN A 749 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 896 GLN A 906 HIS A 914 GLN A1088 HIS A1375 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13480 Z= 0.223 Angle : 0.641 10.824 18250 Z= 0.326 Chirality : 0.042 0.218 2118 Planarity : 0.005 0.057 2323 Dihedral : 5.318 25.589 1810 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.21 % Allowed : 10.18 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1660 helix: -0.96 (0.16), residues: 881 sheet: -0.74 (0.61), residues: 73 loop : -2.06 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 176 HIS 0.006 0.001 HIS A 178 PHE 0.018 0.002 PHE A 163 TYR 0.021 0.002 TYR E 247 ARG 0.004 0.001 ARG E 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 260 average time/residue: 0.3056 time to fit residues: 110.4168 Evaluate side-chains 200 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1528 time to fit residues: 5.3375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 163 optimal weight: 0.0270 chunk 134 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN B 267 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13480 Z= 0.212 Angle : 0.606 10.173 18250 Z= 0.302 Chirality : 0.041 0.150 2118 Planarity : 0.004 0.043 2323 Dihedral : 4.815 24.597 1810 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.34 % Allowed : 12.19 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -1.42 (0.20), residues: 1660 helix: -0.26 (0.17), residues: 885 sheet: -0.36 (0.65), residues: 67 loop : -1.85 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 176 HIS 0.006 0.001 HIS A1034 PHE 0.018 0.001 PHE A 163 TYR 0.023 0.001 TYR E 247 ARG 0.007 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 235 average time/residue: 0.2864 time to fit residues: 95.9988 Evaluate side-chains 195 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1244 time to fit residues: 5.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 487 ASN A 775 HIS A 827 ASN A 896 GLN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13480 Z= 0.175 Angle : 0.576 10.433 18250 Z= 0.285 Chirality : 0.040 0.153 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.496 22.369 1810 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.47 % Allowed : 12.99 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.94 (0.20), residues: 1660 helix: 0.18 (0.17), residues: 886 sheet: -0.30 (0.65), residues: 67 loop : -1.67 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A1034 PHE 0.019 0.001 PHE A1360 TYR 0.011 0.001 TYR A 283 ARG 0.006 0.000 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 220 average time/residue: 0.2840 time to fit residues: 89.2269 Evaluate side-chains 185 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1601 time to fit residues: 4.7823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 4.9990 chunk 91 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 136 optimal weight: 0.0470 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13480 Z= 0.156 Angle : 0.559 9.735 18250 Z= 0.275 Chirality : 0.039 0.149 2118 Planarity : 0.004 0.040 2323 Dihedral : 4.245 20.983 1810 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.74 % Allowed : 13.86 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.54 (0.20), residues: 1660 helix: 0.56 (0.18), residues: 883 sheet: -0.26 (0.65), residues: 67 loop : -1.55 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.005 0.001 HIS A1034 PHE 0.024 0.001 PHE A 163 TYR 0.011 0.001 TYR A 283 ARG 0.007 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 215 average time/residue: 0.2747 time to fit residues: 85.3877 Evaluate side-chains 184 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1301 time to fit residues: 2.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.2980 chunk 144 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A1016 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13480 Z= 0.229 Angle : 0.591 10.008 18250 Z= 0.292 Chirality : 0.041 0.172 2118 Planarity : 0.004 0.045 2323 Dihedral : 4.265 20.752 1810 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.27 % Allowed : 15.07 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.38 (0.20), residues: 1660 helix: 0.68 (0.18), residues: 882 sheet: -0.16 (0.65), residues: 67 loop : -1.45 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.006 0.001 HIS A1034 PHE 0.026 0.001 PHE A 163 TYR 0.013 0.001 TYR A 283 ARG 0.005 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 206 average time/residue: 0.2905 time to fit residues: 85.4881 Evaluate side-chains 189 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1243 time to fit residues: 4.3855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13480 Z= 0.192 Angle : 0.559 9.284 18250 Z= 0.276 Chirality : 0.040 0.145 2118 Planarity : 0.004 0.042 2323 Dihedral : 4.151 20.692 1810 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.94 % Allowed : 15.74 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.13 (0.21), residues: 1660 helix: 0.91 (0.18), residues: 876 sheet: -0.05 (0.64), residues: 67 loop : -1.35 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.006 0.001 HIS A 27 PHE 0.028 0.001 PHE A 163 TYR 0.011 0.001 TYR A 283 ARG 0.004 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 200 average time/residue: 0.2832 time to fit residues: 81.9094 Evaluate side-chains 187 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1351 time to fit residues: 4.0420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS A 487 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13480 Z= 0.186 Angle : 0.566 9.983 18250 Z= 0.278 Chirality : 0.040 0.144 2118 Planarity : 0.004 0.041 2323 Dihedral : 4.098 20.643 1810 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.80 % Allowed : 16.08 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.03 (0.21), residues: 1660 helix: 1.04 (0.18), residues: 876 sheet: 0.06 (0.65), residues: 67 loop : -1.28 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.008 0.001 HIS A 475 PHE 0.027 0.001 PHE A 163 TYR 0.013 0.001 TYR A 283 ARG 0.004 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 194 average time/residue: 0.2792 time to fit residues: 79.2854 Evaluate side-chains 183 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1360 time to fit residues: 3.5076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13480 Z= 0.174 Angle : 0.558 9.898 18250 Z= 0.275 Chirality : 0.040 0.158 2118 Planarity : 0.004 0.045 2323 Dihedral : 4.013 20.436 1810 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.47 % Allowed : 16.28 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.17 (0.21), residues: 1660 helix: 1.16 (0.18), residues: 876 sheet: 0.13 (0.65), residues: 67 loop : -1.22 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1169 HIS 0.006 0.001 HIS A 27 PHE 0.025 0.001 PHE A 163 TYR 0.012 0.001 TYR A 283 ARG 0.004 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 194 average time/residue: 0.2800 time to fit residues: 79.0620 Evaluate side-chains 180 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1444 time to fit residues: 2.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 0.0010 chunk 131 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13480 Z= 0.163 Angle : 0.552 9.772 18250 Z= 0.272 Chirality : 0.040 0.149 2118 Planarity : 0.003 0.039 2323 Dihedral : 3.947 20.427 1810 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.13 % Allowed : 17.08 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.30 (0.21), residues: 1660 helix: 1.26 (0.18), residues: 877 sheet: 0.19 (0.65), residues: 67 loop : -1.15 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 PHE 0.025 0.001 PHE A 163 TYR 0.012 0.001 TYR A 283 ARG 0.004 0.000 ARG C 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 187 average time/residue: 0.2854 time to fit residues: 77.6301 Evaluate side-chains 180 residues out of total 1493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1411 time to fit residues: 2.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 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 = 0.4168 r_free = 0.4168 target = 0.167034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125996 restraints weight = 36995.024| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.45 r_work: 0.3480 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13480 Z= 0.224 Angle : 0.594 9.668 18250 Z= 0.291 Chirality : 0.042 0.227 2118 Planarity : 0.004 0.040 2323 Dihedral : 4.071 20.664 1810 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.20 % Allowed : 17.35 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.20 (0.21), residues: 1660 helix: 1.12 (0.17), residues: 889 sheet: 0.20 (0.64), residues: 67 loop : -1.15 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 PHE 0.023 0.001 PHE A 163 TYR 0.014 0.001 TYR A 283 ARG 0.005 0.000 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.71 seconds wall clock time: 56 minutes 20.05 seconds (3380.05 seconds total)