Starting phenix.real_space_refine on Mon Dec 30 13:48:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_33988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_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/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_33988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_33988.map" model { file = "/net/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_33988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yov_33988/12_2024/7yov_33988.cif" } 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. Time to flip 52 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.23, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.8 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: 1.50 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: 4.07 Time building geometry restraints manager: 3.62 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: 0.00 - 3.50: 17908 3.50 - 6.99: 300 6.99 - 10.49: 35 10.49 - 13.99: 4 13.99 - 17.48: 3 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 3.120 nonbonded pdb=" NH1 ARG E 263 " pdb=" OG1 THR B 261 " model vdw 2.214 3.120 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASP A 245 " model vdw 2.236 3.040 nonbonded pdb=" O GLU A 840 " pdb=" OG SER A1085 " model vdw 2.270 3.040 nonbonded pdb=" O ASP A1094 " pdb=" OG SER A1099 " model vdw 2.279 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.570 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 17 poor density : 356 time to evaluate : 1.557 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 REVERT: E 354 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 234 MET cc_start: 0.3778 (pmm) cc_final: 0.2844 (tpp) REVERT: B 235 MET cc_start: 0.6910 (ppp) cc_final: 0.6531 (ttm) REVERT: A 569 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 1216 LYS cc_start: 0.8173 (mttp) cc_final: 0.7717 (mtmm) outliers start: 17 outliers final: 4 residues processed: 369 average time/residue: 0.3478 time to fit residues: 173.1358 Evaluate side-chains 205 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 824 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN E 279 ASN E 369 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS A 222 ASN A 316 GLN A 328 GLN A 565 GLN A 575 GLN A 648 ASN A 662 ASN A 749 GLN A 775 HIS A 827 ASN A 870 ASN A 896 GLN A 906 HIS A 914 GLN A1088 HIS A1375 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2370 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= 0.209 Angle : 0.646 10.272 18250 Z= 0.331 Chirality : 0.043 0.248 2118 Planarity : 0.005 0.058 2323 Dihedral : 5.751 49.274 1817 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.21 % Allowed : 10.11 % Favored : 87.68 % 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: -2.19 (0.19), residues: 1660 helix: -0.99 (0.16), residues: 879 sheet: -0.73 (0.60), residues: 73 loop : -2.04 (0.22), residues: 708 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 0.017 0.001 PHE A 163 TYR 0.021 0.002 TYR E 247 ARG 0.005 0.001 ARG A 111 *********************** 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 267 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.560 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: C 276 MET cc_start: 0.6910 (mmt) cc_final: 0.6228 (mmt) REVERT: E 283 MET cc_start: 0.7831 (mmt) cc_final: 0.7449 (mmt) REVERT: E 354 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 234 MET cc_start: 0.3324 (pmm) cc_final: 0.2335 (tpp) REVERT: A 323 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8610 (mt) outliers start: 33 outliers final: 14 residues processed: 262 average time/residue: 0.3085 time to fit residues: 112.6793 Evaluate side-chains 207 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS 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: 2.9990 chunk 125 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN B 267 GLN A 48 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 408 ASN A 418 HIS A 652 GLN A 749 GLN A1061 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 13480 Z= 0.498 Angle : 0.809 13.481 18250 Z= 0.401 Chirality : 0.049 0.261 2118 Planarity : 0.006 0.051 2323 Dihedral : 5.834 56.941 1816 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.75 % Allowed : 11.92 % Favored : 84.33 % 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: -1.87 (0.19), residues: 1660 helix: -0.70 (0.16), residues: 880 sheet: -0.41 (0.64), residues: 67 loop : -1.97 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1169 HIS 0.016 0.002 HIS A 669 PHE 0.022 0.003 PHE A1360 TYR 0.030 0.003 TYR A 530 ARG 0.009 0.001 ARG E 241 *********************** 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 264 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.748 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: C 276 MET cc_start: 0.7369 (mmt) cc_final: 0.6903 (mtp) REVERT: B 234 MET cc_start: 0.3058 (pmm) cc_final: 0.2296 (tpp) REVERT: A 35 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 101 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 359 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 762 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5591 (tmm-80) REVERT: A 1313 TYR cc_start: 0.6677 (p90) cc_final: 0.6404 (p90) REVERT: A 1334 LYS cc_start: 0.8195 (mttt) cc_final: 0.7805 (tptt) outliers start: 56 outliers final: 33 residues processed: 251 average time/residue: 0.3306 time to fit residues: 116.9394 Evaluate side-chains 220 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1174 SER Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 160 optimal weight: 0.0010 chunk 79 optimal weight: 0.2980 chunk 143 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN A1375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13480 Z= 0.168 Angle : 0.583 9.508 18250 Z= 0.293 Chirality : 0.041 0.213 2118 Planarity : 0.004 0.048 2323 Dihedral : 4.941 46.828 1812 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.21 % Allowed : 14.00 % Favored : 83.79 % 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: -1.16 (0.20), residues: 1660 helix: -0.06 (0.17), residues: 899 sheet: -0.83 (0.62), residues: 72 loop : -1.67 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 176 HIS 0.005 0.001 HIS A1034 PHE 0.020 0.001 PHE A1360 TYR 0.013 0.001 TYR A1119 ARG 0.005 0.000 ARG E 300 *********************** 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 238 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6778 (ptm) REVERT: E 272 SER cc_start: 0.8040 (m) cc_final: 0.7282 (t) REVERT: B 234 MET cc_start: 0.3030 (pmm) cc_final: 0.2556 (tpp) REVERT: A 35 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 241 MET cc_start: 0.8584 (mmm) cc_final: 0.8290 (mmm) REVERT: A 388 MET cc_start: 0.9205 (tpp) cc_final: 0.8919 (tpp) outliers start: 33 outliers final: 17 residues processed: 231 average time/residue: 0.3043 time to fit residues: 99.2848 Evaluate side-chains 200 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1287 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 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: 0.7574 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13480 Z= 0.199 Angle : 0.595 9.339 18250 Z= 0.295 Chirality : 0.041 0.211 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.722 46.701 1812 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.61 % Allowed : 14.00 % Favored : 83.39 % 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: -0.80 (0.20), residues: 1660 helix: 0.26 (0.17), residues: 897 sheet: -0.42 (0.62), residues: 67 loop : -1.55 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A1034 PHE 0.014 0.001 PHE A1360 TYR 0.012 0.001 TYR A 283 ARG 0.009 0.001 ARG A 762 *********************** 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 239 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 276 MET cc_start: 0.6659 (mtp) cc_final: 0.6205 (mtp) REVERT: D 304 LYS cc_start: 0.6561 (mttp) cc_final: 0.6324 (mttp) REVERT: C 262 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6763 (ptm) REVERT: C 276 MET cc_start: 0.7426 (ttm) cc_final: 0.7182 (mtp) REVERT: E 329 ASN cc_start: 0.7955 (t0) cc_final: 0.7731 (t0) REVERT: B 234 MET cc_start: 0.2861 (pmm) cc_final: 0.2529 (tpp) REVERT: B 270 LYS cc_start: 0.8437 (tppp) cc_final: 0.7859 (tmmt) REVERT: A 35 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7270 (mp) REVERT: A 388 MET cc_start: 0.9190 (tpp) cc_final: 0.8946 (tpp) REVERT: A 1220 ARG cc_start: 0.7753 (ptm160) cc_final: 0.7384 (ptm-80) REVERT: A 1334 LYS cc_start: 0.8114 (mttt) cc_final: 0.7679 (tptt) outliers start: 39 outliers final: 24 residues processed: 233 average time/residue: 0.2732 time to fit residues: 91.9407 Evaluate side-chains 213 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.5980 chunk 144 optimal weight: 0.0070 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.0030 chunk 39 optimal weight: 0.0010 chunk 160 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 154 optimal weight: 3.9990 overall best weight: 0.1232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS A 231 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13480 Z= 0.143 Angle : 0.542 9.324 18250 Z= 0.272 Chirality : 0.040 0.205 2118 Planarity : 0.004 0.040 2323 Dihedral : 4.389 44.256 1812 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.01 % Allowed : 15.67 % Favored : 82.32 % 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: -0.36 (0.21), residues: 1660 helix: 0.70 (0.18), residues: 889 sheet: -0.27 (0.63), residues: 67 loop : -1.46 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.004 0.001 HIS A1034 PHE 0.023 0.001 PHE A 163 TYR 0.013 0.001 TYR A 871 ARG 0.007 0.000 ARG A1093 *********************** 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 246 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 276 MET cc_start: 0.6611 (mtp) cc_final: 0.6157 (mtp) REVERT: C 249 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.6897 (mm) REVERT: E 263 ARG cc_start: 0.7790 (mmp80) cc_final: 0.7305 (mmp-170) REVERT: B 234 MET cc_start: 0.2467 (pmm) cc_final: 0.2250 (tpp) REVERT: B 283 MET cc_start: 0.8486 (tpp) cc_final: 0.7888 (tpt) REVERT: A 35 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 241 MET cc_start: 0.8609 (mmm) cc_final: 0.8348 (mmm) REVERT: A 388 MET cc_start: 0.9197 (tpp) cc_final: 0.8978 (tpp) REVERT: A 1013 THR cc_start: 0.8753 (p) cc_final: 0.8485 (p) REVERT: A 1220 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7242 (ptm-80) REVERT: A 1334 LYS cc_start: 0.8065 (mttt) cc_final: 0.7646 (tptt) outliers start: 30 outliers final: 14 residues processed: 240 average time/residue: 0.2784 time to fit residues: 96.3047 Evaluate side-chains 202 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 GLN D 279 ASN A 11 HIS A 166 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13480 Z= 0.207 Angle : 0.593 14.538 18250 Z= 0.292 Chirality : 0.041 0.199 2118 Planarity : 0.004 0.042 2323 Dihedral : 4.381 46.509 1812 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.55 % Allowed : 15.74 % Favored : 81.71 % 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: 0.71 (0.17), residues: 893 sheet: -0.28 (0.62), residues: 67 loop : -1.38 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A 659 PHE 0.027 0.001 PHE A 163 TYR 0.013 0.001 TYR A 871 ARG 0.010 0.000 ARG C 263 *********************** 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 229 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7196 (mm) REVERT: A 35 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7485 (mp) REVERT: A 1220 ARG cc_start: 0.7616 (ptm160) cc_final: 0.7237 (ptm-80) REVERT: A 1229 TYR cc_start: 0.7746 (m-80) cc_final: 0.7430 (m-80) outliers start: 38 outliers final: 21 residues processed: 220 average time/residue: 0.3039 time to fit residues: 97.2090 Evaluate side-chains 207 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1321 LEU 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: 2.9990 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13480 Z= 0.226 Angle : 0.603 12.569 18250 Z= 0.299 Chirality : 0.042 0.211 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.452 46.814 1812 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.21 % Allowed : 16.61 % Favored : 81.18 % 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: -0.28 (0.21), residues: 1660 helix: 0.70 (0.17), residues: 899 sheet: -0.22 (0.62), residues: 67 loop : -1.35 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A 669 PHE 0.028 0.001 PHE A 163 TYR 0.016 0.001 TYR A 871 ARG 0.004 0.000 ARG A 677 *********************** 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 218 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7155 (mm) REVERT: A 35 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 871 TYR cc_start: 0.7052 (t80) cc_final: 0.6803 (t80) REVERT: A 1220 ARG cc_start: 0.7613 (ptm160) cc_final: 0.7224 (ptm-80) outliers start: 33 outliers final: 27 residues processed: 211 average time/residue: 0.3171 time to fit residues: 95.7226 Evaluate side-chains 207 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN D 279 ASN A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4309 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= 0.224 Angle : 0.614 11.989 18250 Z= 0.305 Chirality : 0.042 0.203 2118 Planarity : 0.004 0.044 2323 Dihedral : 4.443 46.586 1812 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.21 % Allowed : 16.48 % Favored : 81.31 % 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: -0.26 (0.21), residues: 1660 helix: 0.72 (0.17), residues: 898 sheet: -0.18 (0.62), residues: 67 loop : -1.34 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A 659 PHE 0.031 0.001 PHE A 163 TYR 0.015 0.001 TYR A1313 ARG 0.005 0.000 ARG C 263 *********************** 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 216 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 35 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 871 TYR cc_start: 0.7053 (t80) cc_final: 0.6779 (t80) REVERT: A 1220 ARG cc_start: 0.7586 (ptm160) cc_final: 0.7212 (ptm-80) outliers start: 33 outliers final: 26 residues processed: 209 average time/residue: 0.2956 time to fit residues: 89.2359 Evaluate side-chains 202 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.0010 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13480 Z= 0.182 Angle : 0.597 11.609 18250 Z= 0.298 Chirality : 0.041 0.220 2118 Planarity : 0.004 0.038 2323 Dihedral : 4.330 44.535 1812 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.21 % Allowed : 16.68 % Favored : 81.11 % 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: -0.14 (0.21), residues: 1660 helix: 0.82 (0.17), residues: 898 sheet: -0.16 (0.62), residues: 67 loop : -1.28 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS A1034 PHE 0.029 0.001 PHE A 163 TYR 0.011 0.001 TYR A 283 ARG 0.007 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 222 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7338 (mm) REVERT: A 35 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 294 TYR cc_start: 0.8491 (m-10) cc_final: 0.8258 (m-10) REVERT: A 871 TYR cc_start: 0.7023 (t80) cc_final: 0.6800 (t80) REVERT: A 1220 ARG cc_start: 0.7559 (ptm160) cc_final: 0.7127 (ptm-80) REVERT: A 1229 TYR cc_start: 0.7520 (m-80) cc_final: 0.7181 (m-80) outliers start: 33 outliers final: 29 residues processed: 215 average time/residue: 0.2812 time to fit residues: 87.7128 Evaluate side-chains 208 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0060 chunk 40 optimal weight: 0.3980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 131 optimal weight: 0.0670 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN A 11 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.170968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139243 restraints weight = 36454.364| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.13 r_work: 0.3482 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13480 Z= 0.148 Angle : 0.575 11.119 18250 Z= 0.286 Chirality : 0.040 0.197 2118 Planarity : 0.004 0.039 2323 Dihedral : 4.072 40.219 1812 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.54 % Allowed : 17.62 % Favored : 80.84 % 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: 0.18 (0.21), residues: 1660 helix: 1.12 (0.18), residues: 892 sheet: -0.15 (0.63), residues: 67 loop : -1.16 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.004 0.001 HIS A1034 PHE 0.029 0.001 PHE A 163 TYR 0.011 0.001 TYR A 283 ARG 0.009 0.000 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.07 seconds wall clock time: 57 minutes 21.02 seconds (3441.02 seconds total)