Starting phenix.real_space_refine on Fri Mar 6 17:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.map" model { file = "/net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q97_13867/03_2026/7q97_13867.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 10622 2.51 5 N 3150 2.21 5 O 3258 1.98 5 H 15752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32806 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 16403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1047, 16401 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 35, 'TRANS': 1011} Chain breaks: 9 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 16592 Restraints were copied for chains: B Time building chain proxies: 33.48, per 1000 atoms: 1.02 Number of scatterers: 32806 At special positions: 0 Unit cell: (141.05, 128.31, 90.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 3258 8.00 N 3150 7.00 C 10622 6.00 H 15752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 16 sheets defined 4.2% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.620A pdb=" N THR A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 1110 through 1115 removed outlier: 3.821A pdb=" N LYS A1113 " --> pdb=" O ASP A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1123 Processing helix chain 'A' and resid 1193 through 1195 No H-bonds generated for 'chain 'A' and resid 1193 through 1195' Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1327 through 1331 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.620A pdb=" N THR B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 1110 through 1115 removed outlier: 3.821A pdb=" N LYS B1113 " --> pdb=" O ASP B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1123 Processing helix chain 'B' and resid 1193 through 1195 No H-bonds generated for 'chain 'B' and resid 1193 through 1195' Processing helix chain 'B' and resid 1238 through 1242 Processing helix chain 'B' and resid 1327 through 1331 Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.493A pdb=" N PHE A 323 " --> pdb=" O TRP A 333 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 331 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 385 removed outlier: 6.093A pdb=" N LEU A 372 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 359 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 360 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 430 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 425 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N SER A 430 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N GLU A 423 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LEU A 432 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEU A 421 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LEU A 434 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 13.272A pdb=" N TYR A 419 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 410 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 385 removed outlier: 6.093A pdb=" N LEU A 372 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 359 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 360 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 430 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 12.912A pdb=" N ARG A 433 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N TYR A 449 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 435 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 446 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU A 458 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU A 448 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N ARG A 454 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N TYR A 471 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 458 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 467 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A 466 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA A 480 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 496 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 482 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 506 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 517 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP A 510 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 515 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 529 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 528 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 554 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 543 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 552 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N ARG A 551 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR A 567 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR A 553 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 585 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR A 597 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A 587 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL A 595 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 617 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 610 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 615 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N GLN A 614 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N TYR A 630 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A 616 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 627 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU A 639 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 629 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE A 637 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER A 648 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 661 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 650 " --> pdb=" O GLN A 659 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLN A 659 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 680 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 702 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL A 701 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A 712 " --> pdb=" O HIS A 724 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS A 724 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 714 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU A 722 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A 743 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 764 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 775 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG A 806 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 828 " --> pdb=" O ASP A 819 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 827 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A 848 " --> pdb=" O TYR A 860 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 857 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 873 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 859 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 871 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A 869 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 906 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR A 926 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A 951 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 961 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 971 " --> pdb=" O ARG A 983 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 993 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 992 " --> pdb=" O PHE A1004 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A1002 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A1003 " --> pdb=" O THR A1016 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL A1013 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG A1033 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL A1063 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A1075 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP A1091 " --> pdb=" O ARG A1075 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A1077 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A1089 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS A1079 " --> pdb=" O ILE A1087 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1126 through 1127 removed outlier: 3.874A pdb=" N GLU A1142 " --> pdb=" O ARG A1133 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A1141 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A1150 " --> pdb=" O GLN A1167 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A1167 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1163 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A1162 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A1187 " --> pdb=" O ARG A1178 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A1186 " --> pdb=" O ARG A1202 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG A1202 " --> pdb=" O ILE A1186 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A1188 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A1200 " --> pdb=" O LYS A1188 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU A1190 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A1211 " --> pdb=" O TYR A1222 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1232 " --> pdb=" O TYR A1247 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1257 " --> pdb=" O HIS A1248 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A1256 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A1267 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN A1268 " --> pdb=" O ILE A1281 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE A1281 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A1270 " --> pdb=" O GLU A1279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1313 through 1314 removed outlier: 3.549A pdb=" N ARG A1319 " --> pdb=" O ASP A1314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1344 through 1345 Processing sheet with id=AA9, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.493A pdb=" N PHE B 323 " --> pdb=" O TRP B 333 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 331 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 381 through 385 removed outlier: 6.094A pdb=" N LEU B 372 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 359 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 360 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 430 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 425 " --> pdb=" O ASP B 428 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N SER B 430 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N GLU B 423 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LEU B 432 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEU B 421 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N LEU B 434 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 13.272A pdb=" N TYR B 419 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 410 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 381 through 385 removed outlier: 6.094A pdb=" N LEU B 372 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 359 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 360 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 430 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 12.912A pdb=" N ARG B 433 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N TYR B 449 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER B 435 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS B 446 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 458 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 448 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N ARG B 454 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N TYR B 471 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP B 456 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 458 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 467 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLN B 466 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA B 480 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 496 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 482 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA B 506 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 517 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 510 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 515 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 529 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE B 528 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 554 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR B 543 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 552 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N ARG B 551 " --> pdb=" O TYR B 567 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR B 567 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR B 553 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG B 585 " --> pdb=" O TYR B 597 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 597 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 587 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL B 595 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 617 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 610 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 615 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N GLN B 614 " --> pdb=" O TYR B 630 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N TYR B 630 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 616 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 627 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 639 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 629 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE B 637 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER B 648 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU B 661 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 650 " --> pdb=" O GLN B 659 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN B 659 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE B 680 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 702 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL B 701 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS B 712 " --> pdb=" O HIS B 724 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N HIS B 724 " --> pdb=" O LYS B 712 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 714 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 722 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS B 743 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 764 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 775 " --> pdb=" O THR B 788 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG B 806 " --> pdb=" O PHE B 818 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 828 " --> pdb=" O ASP B 819 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 827 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER B 848 " --> pdb=" O TYR B 860 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 857 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B 873 " --> pdb=" O ALA B 857 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 859 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 871 " --> pdb=" O ARG B 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 861 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B 869 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 906 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR B 926 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU B 951 " --> pdb=" O HIS B 962 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 961 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR B 971 " --> pdb=" O ARG B 983 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 993 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 992 " --> pdb=" O PHE B1004 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B1002 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B1003 " --> pdb=" O THR B1016 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL B1013 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG B1033 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL B1063 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B1075 " --> pdb=" O ASP B1091 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP B1091 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B1077 " --> pdb=" O SER B1089 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER B1089 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS B1079 " --> pdb=" O ILE B1087 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1126 through 1127 removed outlier: 3.875A pdb=" N GLU B1142 " --> pdb=" O ARG B1133 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE B1141 " --> pdb=" O PHE B1153 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B1150 " --> pdb=" O GLN B1167 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B1167 " --> pdb=" O VAL B1150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B1163 " --> pdb=" O ALA B1154 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE B1162 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B1187 " --> pdb=" O ARG B1178 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B1186 " --> pdb=" O ARG B1202 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG B1202 " --> pdb=" O ILE B1186 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B1188 " --> pdb=" O GLU B1200 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU B1200 " --> pdb=" O LYS B1188 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU B1190 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B1211 " --> pdb=" O TYR B1222 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B1232 " --> pdb=" O TYR B1247 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B1257 " --> pdb=" O HIS B1248 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN B1256 " --> pdb=" O ALA B1269 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B1267 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B1268 " --> pdb=" O ILE B1281 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B1281 " --> pdb=" O GLN B1268 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B1270 " --> pdb=" O GLU B1279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1313 through 1314 removed outlier: 3.549A pdb=" N ARG B1319 " --> pdb=" O ASP B1314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1344 through 1345 558 hydrogen bonds defined for protein. 1542 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: 9.44 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15740 1.03 - 1.23: 25 1.23 - 1.42: 7875 1.42 - 1.62: 9516 1.62 - 1.81: 36 Bond restraints: 33192 Sorted by residual: bond pdb=" CG LEU A 826 " pdb=" CD1 LEU A 826 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CG LEU B 826 " pdb=" CD1 LEU B 826 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG LEU B 505 " pdb=" CD1 LEU B 505 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" CG LEU A 505 " pdb=" CD1 LEU A 505 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB ILE B1317 " pdb=" CG2 ILE B1317 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 ... (remaining 33187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 56090 1.30 - 2.60: 2833 2.60 - 3.90: 186 3.90 - 5.20: 21 5.20 - 6.50: 6 Bond angle restraints: 59136 Sorted by residual: angle pdb=" N PRO B 731 " pdb=" CA PRO B 731 " pdb=" C PRO B 731 " ideal model delta sigma weight residual 111.68 114.97 -3.29 1.67e+00 3.59e-01 3.89e+00 angle pdb=" N PRO A 731 " pdb=" CA PRO A 731 " pdb=" C PRO A 731 " ideal model delta sigma weight residual 111.68 114.97 -3.29 1.67e+00 3.59e-01 3.87e+00 angle pdb=" CA LEU A 445 " pdb=" CB LEU A 445 " pdb=" CG LEU A 445 " ideal model delta sigma weight residual 116.30 122.80 -6.50 3.50e+00 8.16e-02 3.45e+00 angle pdb=" CA LEU B 445 " pdb=" CB LEU B 445 " pdb=" CG LEU B 445 " ideal model delta sigma weight residual 116.30 122.78 -6.48 3.50e+00 8.16e-02 3.43e+00 angle pdb=" N ALA B 638 " pdb=" CA ALA B 638 " pdb=" C ALA B 638 " ideal model delta sigma weight residual 109.06 112.16 -3.10 1.70e+00 3.46e-01 3.33e+00 ... (remaining 59131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14899 17.86 - 35.73: 607 35.73 - 53.59: 159 53.59 - 71.46: 39 71.46 - 89.32: 10 Dihedral angle restraints: 15714 sinusoidal: 8446 harmonic: 7268 Sorted by residual: dihedral pdb=" CA TYR A 985 " pdb=" C TYR A 985 " pdb=" N TYR A 986 " pdb=" CA TYR A 986 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA TYR B 985 " pdb=" C TYR B 985 " pdb=" N TYR B 986 " pdb=" CA TYR B 986 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU B 991 " pdb=" C LEU B 991 " pdb=" N HIS B 992 " pdb=" CA HIS B 992 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 15711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1400 0.032 - 0.064: 614 0.064 - 0.095: 288 0.095 - 0.127: 99 0.127 - 0.159: 15 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA PRO B 305 " pdb=" N PRO B 305 " pdb=" C PRO B 305 " pdb=" CB PRO B 305 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PRO A 305 " pdb=" N PRO A 305 " pdb=" C PRO A 305 " pdb=" CB PRO A 305 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL B 902 " pdb=" N VAL B 902 " pdb=" C VAL B 902 " pdb=" CB VAL B 902 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 2413 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B1283 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO B1284 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1284 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1284 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1283 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO A1284 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1035 " 0.107 9.50e-02 1.11e+02 3.59e-02 1.45e+00 pdb=" NE ARG A1035 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A1035 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1035 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1035 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A1035 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A1035 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1035 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1035 " 0.001 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1182 2.15 - 2.76: 61107 2.76 - 3.38: 78518 3.38 - 3.99: 109224 3.99 - 4.60: 172516 Nonbonded interactions: 422547 Sorted by model distance: nonbonded pdb=" O ILE B 594 " pdb=" HE1 TRP B 609 " model vdw 1.539 2.450 nonbonded pdb=" O ILE A 594 " pdb=" HE1 TRP A 609 " model vdw 1.540 2.450 nonbonded pdb=" OD1 ASP B1007 " pdb=" H ARG B1011 " model vdw 1.549 2.450 nonbonded pdb=" OD1 ASP A1007 " pdb=" H ARG A1011 " model vdw 1.550 2.450 nonbonded pdb=" O LEU B 905 " pdb=" HH TYR B 919 " model vdw 1.553 2.450 ... (remaining 422542 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.590 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: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 61.330 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.009 0.060 17440 Z= 0.355 Angle : 0.648 6.499 23610 Z= 0.334 Chirality : 0.045 0.159 2416 Planarity : 0.005 0.054 3164 Dihedral : 10.047 89.324 6448 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 0.56 % Allowed : 2.03 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2054 helix: -0.24 (1.16), residues: 20 sheet: 1.47 (0.21), residues: 650 loop : -0.88 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1185 TYR 0.017 0.002 TYR A 837 PHE 0.010 0.002 PHE B 818 TRP 0.009 0.002 TRP B 605 HIS 0.007 0.001 HIS B 555 Details of bonding type rmsd covalent geometry : bond 0.00902 (17440) covalent geometry : angle 0.64777 (23610) hydrogen bonds : bond 0.17308 ( 542) hydrogen bonds : angle 6.77950 ( 1542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 367 time to evaluate : 0.698 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 SER cc_start: 0.7796 (p) cc_final: 0.7467 (p) REVERT: A 1027 ASP cc_start: 0.7032 (m-30) cc_final: 0.6799 (m-30) REVERT: A 1202 ARG cc_start: 0.6799 (ptp-170) cc_final: 0.6539 (mmm160) REVERT: B 428 ASP cc_start: 0.5831 (t0) cc_final: 0.5579 (t0) REVERT: B 451 SER cc_start: 0.8005 (p) cc_final: 0.7686 (p) REVERT: B 1009 LEU cc_start: 0.7021 (mp) cc_final: 0.6802 (mp) REVERT: B 1027 ASP cc_start: 0.6960 (m-30) cc_final: 0.6697 (m-30) outliers start: 10 outliers final: 2 residues processed: 377 average time/residue: 0.4044 time to fit residues: 209.4717 Evaluate side-chains 229 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 758 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.0060 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 GLN A1218 GLN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 GLN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150571 restraints weight = 54324.492| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.79 r_work: 0.3616 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17440 Z= 0.111 Angle : 0.524 5.828 23610 Z= 0.279 Chirality : 0.040 0.151 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.647 59.562 2396 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 0.84 % Allowed : 6.53 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2054 helix: 0.08 (1.25), residues: 20 sheet: 1.41 (0.19), residues: 784 loop : -0.83 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 772 TYR 0.012 0.001 TYR B1286 PHE 0.007 0.001 PHE B 930 TRP 0.019 0.001 TRP A 669 HIS 0.007 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00253 (17440) covalent geometry : angle 0.52351 (23610) hydrogen bonds : bond 0.03571 ( 542) hydrogen bonds : angle 4.99795 ( 1542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: A 551 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.8026 (mtt90) REVERT: A 1027 ASP cc_start: 0.7555 (m-30) cc_final: 0.7214 (m-30) REVERT: A 1202 ARG cc_start: 0.7154 (ptp-170) cc_final: 0.6506 (mmm160) REVERT: A 1206 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7505 (p0) REVERT: B 439 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6305 (m-30) REVERT: B 551 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.8037 (mtt90) REVERT: B 1027 ASP cc_start: 0.7513 (m-30) cc_final: 0.7178 (m-30) outliers start: 15 outliers final: 7 residues processed: 262 average time/residue: 0.4430 time to fit residues: 156.3826 Evaluate side-chains 224 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1166 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS ** B1276 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 = 0.3955 r_free = 0.3955 target = 0.168134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149530 restraints weight = 53995.703| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.71 r_work: 0.3615 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17440 Z= 0.151 Angle : 0.533 4.976 23610 Z= 0.285 Chirality : 0.040 0.149 2416 Planarity : 0.004 0.052 3164 Dihedral : 4.471 19.820 2392 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.46 % Allowed : 7.94 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2054 helix: -0.20 (1.26), residues: 20 sheet: 1.39 (0.19), residues: 748 loop : -1.03 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 778 TYR 0.015 0.002 TYR A1286 PHE 0.007 0.001 PHE B1310 TRP 0.020 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00354 (17440) covalent geometry : angle 0.53274 (23610) hydrogen bonds : bond 0.04022 ( 542) hydrogen bonds : angle 4.74747 ( 1542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.891 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: A 551 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.8081 (mtt90) REVERT: A 762 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7806 (mmp-170) REVERT: A 1027 ASP cc_start: 0.7566 (m-30) cc_final: 0.7240 (m-30) REVERT: A 1206 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7693 (p0) REVERT: B 551 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8090 (mtt90) REVERT: B 762 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7803 (mmp-170) REVERT: B 1027 ASP cc_start: 0.7540 (m-30) cc_final: 0.7234 (m-30) outliers start: 26 outliers final: 17 residues processed: 225 average time/residue: 0.4521 time to fit residues: 136.7842 Evaluate side-chains 211 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 1037 GLN Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 121 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A1249 ASN A1252 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151850 restraints weight = 53636.911| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.58 r_work: 0.3645 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17440 Z= 0.126 Angle : 0.502 4.642 23610 Z= 0.270 Chirality : 0.039 0.141 2416 Planarity : 0.003 0.051 3164 Dihedral : 4.359 18.922 2392 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 1.24 % Allowed : 8.45 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2054 helix: -0.29 (1.25), residues: 20 sheet: 1.40 (0.19), residues: 750 loop : -1.18 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.013 0.001 TYR A1286 PHE 0.016 0.001 PHE A1458 TRP 0.024 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00292 (17440) covalent geometry : angle 0.50201 (23610) hydrogen bonds : bond 0.03428 ( 542) hydrogen bonds : angle 4.62589 ( 1542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.889 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: A 548 GLN cc_start: 0.6034 (mp10) cc_final: 0.5829 (mp10) REVERT: A 551 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8192 (mtt90) REVERT: A 1027 ASP cc_start: 0.7482 (m-30) cc_final: 0.7148 (m-30) REVERT: B 548 GLN cc_start: 0.6108 (mp10) cc_final: 0.5887 (mp10) REVERT: B 551 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.8199 (mtt90) REVERT: B 1027 ASP cc_start: 0.7459 (m-30) cc_final: 0.7143 (m-30) outliers start: 22 outliers final: 20 residues processed: 216 average time/residue: 0.4144 time to fit residues: 122.3349 Evaluate side-chains 214 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 1037 GLN Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 204 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 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 = 0.3816 r_free = 0.3816 target = 0.157983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139180 restraints weight = 54275.100| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.74 r_work: 0.3481 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17440 Z= 0.160 Angle : 0.535 5.230 23610 Z= 0.288 Chirality : 0.040 0.143 2416 Planarity : 0.004 0.053 3164 Dihedral : 4.527 18.877 2392 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 1.75 % Allowed : 8.39 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2054 helix: -0.57 (1.26), residues: 20 sheet: 1.32 (0.19), residues: 760 loop : -1.30 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.014 0.002 TYR B 374 PHE 0.012 0.001 PHE B1458 TRP 0.019 0.001 TRP B 669 HIS 0.006 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00376 (17440) covalent geometry : angle 0.53474 (23610) hydrogen bonds : bond 0.03929 ( 542) hydrogen bonds : angle 4.71912 ( 1542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.853 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: A 548 GLN cc_start: 0.6167 (mp10) cc_final: 0.5939 (mp10) REVERT: A 551 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8230 (mtt90) REVERT: A 1027 ASP cc_start: 0.7507 (m-30) cc_final: 0.7172 (m-30) REVERT: A 1214 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: B 548 GLN cc_start: 0.6146 (mp10) cc_final: 0.5906 (mp10) REVERT: B 551 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8224 (mtt90) REVERT: B 1027 ASP cc_start: 0.7528 (m-30) cc_final: 0.7179 (m-30) REVERT: B 1236 ASP cc_start: 0.6440 (m-30) cc_final: 0.6230 (m-30) REVERT: B 1288 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7154 (mt-10) outliers start: 31 outliers final: 25 residues processed: 221 average time/residue: 0.3931 time to fit residues: 120.8585 Evaluate side-chains 219 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1252 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139407 restraints weight = 54388.327| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.73 r_work: 0.3478 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17440 Z= 0.157 Angle : 0.526 5.152 23610 Z= 0.283 Chirality : 0.040 0.139 2416 Planarity : 0.004 0.059 3164 Dihedral : 4.532 18.438 2392 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 1.80 % Allowed : 8.61 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2054 helix: -0.66 (1.25), residues: 20 sheet: 1.23 (0.19), residues: 732 loop : -1.36 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.013 0.002 TYR B 374 PHE 0.009 0.001 PHE A1458 TRP 0.022 0.001 TRP A 669 HIS 0.006 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00371 (17440) covalent geometry : angle 0.52562 (23610) hydrogen bonds : bond 0.03770 ( 542) hydrogen bonds : angle 4.71093 ( 1542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.829 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: A 548 GLN cc_start: 0.6130 (mp10) cc_final: 0.5924 (mp10) REVERT: A 551 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8255 (mtt180) REVERT: A 762 ARG cc_start: 0.8436 (mtp180) cc_final: 0.7754 (mmp-170) REVERT: A 1027 ASP cc_start: 0.7528 (m-30) cc_final: 0.7184 (m-30) REVERT: A 1214 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: B 548 GLN cc_start: 0.6129 (mp10) cc_final: 0.5906 (mp10) REVERT: B 551 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.8244 (mtt90) REVERT: B 762 ARG cc_start: 0.8427 (mtp180) cc_final: 0.7735 (mmp-170) REVERT: B 1027 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (m-30) outliers start: 32 outliers final: 29 residues processed: 204 average time/residue: 0.3667 time to fit residues: 104.8484 Evaluate side-chains 218 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 142 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1252 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1249 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 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 = 0.3781 r_free = 0.3781 target = 0.155135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136157 restraints weight = 55210.872| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.76 r_work: 0.3437 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17440 Z= 0.253 Angle : 0.618 6.215 23610 Z= 0.334 Chirality : 0.042 0.153 2416 Planarity : 0.005 0.063 3164 Dihedral : 5.000 23.933 2392 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.45 % Rotamer: Outliers : 2.20 % Allowed : 8.61 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2054 helix: -1.69 (1.06), residues: 20 sheet: 0.85 (0.19), residues: 746 loop : -1.59 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.017 0.002 TYR B 374 PHE 0.012 0.002 PHE A 545 TRP 0.018 0.002 TRP B 669 HIS 0.008 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00600 (17440) covalent geometry : angle 0.61808 (23610) hydrogen bonds : bond 0.04816 ( 542) hydrogen bonds : angle 5.06697 ( 1542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLN cc_start: 0.6133 (mp10) cc_final: 0.5898 (mp10) REVERT: A 551 ARG cc_start: 0.8675 (mtt-85) cc_final: 0.8262 (mtt90) REVERT: A 762 ARG cc_start: 0.8440 (mtp180) cc_final: 0.7735 (mmp-170) REVERT: A 1027 ASP cc_start: 0.7579 (m-30) cc_final: 0.7239 (m-30) REVERT: A 1214 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: B 548 GLN cc_start: 0.6136 (mp10) cc_final: 0.5859 (mp10) REVERT: B 551 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.8302 (mtt180) REVERT: B 762 ARG cc_start: 0.8425 (mtp180) cc_final: 0.7730 (mmp-170) REVERT: B 990 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6414 (p90) REVERT: B 1027 ASP cc_start: 0.7576 (m-30) cc_final: 0.7231 (m-30) outliers start: 39 outliers final: 34 residues processed: 202 average time/residue: 0.3466 time to fit residues: 99.5478 Evaluate side-chains 211 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 TRP Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1206 ASP Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 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 = 0.3809 r_free = 0.3809 target = 0.157418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137839 restraints weight = 54699.783| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.84 r_work: 0.3459 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17440 Z= 0.144 Angle : 0.523 5.033 23610 Z= 0.283 Chirality : 0.039 0.137 2416 Planarity : 0.004 0.059 3164 Dihedral : 4.641 18.385 2392 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 1.69 % Allowed : 9.01 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2054 helix: -1.22 (1.12), residues: 20 sheet: 1.02 (0.20), residues: 722 loop : -1.53 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.013 0.001 TYR B1286 PHE 0.008 0.001 PHE A1458 TRP 0.020 0.001 TRP B 669 HIS 0.006 0.001 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00340 (17440) covalent geometry : angle 0.52260 (23610) hydrogen bonds : bond 0.03712 ( 542) hydrogen bonds : angle 4.78863 ( 1542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.932 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: A 548 GLN cc_start: 0.6081 (mp10) cc_final: 0.5812 (mp10) REVERT: A 551 ARG cc_start: 0.8643 (mtt-85) cc_final: 0.8239 (mtt90) REVERT: A 1027 ASP cc_start: 0.7533 (m-30) cc_final: 0.7189 (m-30) REVERT: A 1214 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: B 548 GLN cc_start: 0.6111 (mp10) cc_final: 0.5836 (mp10) REVERT: B 551 ARG cc_start: 0.8637 (mtt-85) cc_final: 0.8235 (mtt90) REVERT: B 1027 ASP cc_start: 0.7544 (m-30) cc_final: 0.7182 (m-30) REVERT: B 1288 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7262 (mt-10) outliers start: 30 outliers final: 28 residues processed: 195 average time/residue: 0.3808 time to fit residues: 104.3840 Evaluate side-chains 205 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139608 restraints weight = 54513.171| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.73 r_work: 0.3481 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17440 Z= 0.124 Angle : 0.505 4.817 23610 Z= 0.273 Chirality : 0.039 0.137 2416 Planarity : 0.004 0.058 3164 Dihedral : 4.430 17.953 2392 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 1.69 % Allowed : 9.12 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2054 helix: -0.84 (1.19), residues: 20 sheet: 1.04 (0.20), residues: 726 loop : -1.45 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.011 0.001 TYR B 374 PHE 0.008 0.001 PHE A1458 TRP 0.026 0.001 TRP A 669 HIS 0.006 0.001 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00292 (17440) covalent geometry : angle 0.50508 (23610) hydrogen bonds : bond 0.03441 ( 542) hydrogen bonds : angle 4.63418 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.829 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: A 551 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8267 (mtt90) REVERT: A 762 ARG cc_start: 0.8464 (mtm110) cc_final: 0.7615 (mmp-170) REVERT: A 1027 ASP cc_start: 0.7509 (m-30) cc_final: 0.7165 (m-30) REVERT: A 1214 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: B 551 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8262 (mtt90) REVERT: B 762 ARG cc_start: 0.8455 (mtm110) cc_final: 0.7659 (mmp-170) REVERT: B 1027 ASP cc_start: 0.7523 (m-30) cc_final: 0.7160 (m-30) REVERT: B 1288 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7178 (mt-10) outliers start: 30 outliers final: 29 residues processed: 197 average time/residue: 0.3484 time to fit residues: 97.9139 Evaluate side-chains 209 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 114 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1276 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 = 0.3844 r_free = 0.3844 target = 0.160218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141574 restraints weight = 54460.176| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.73 r_work: 0.3508 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17440 Z= 0.085 Angle : 0.475 4.796 23610 Z= 0.257 Chirality : 0.038 0.132 2416 Planarity : 0.003 0.053 3164 Dihedral : 4.210 17.130 2392 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.69 % Allowed : 9.12 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2054 helix: -0.38 (1.26), residues: 20 sheet: 1.18 (0.20), residues: 726 loop : -1.36 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.010 0.001 TYR B1286 PHE 0.008 0.001 PHE A1458 TRP 0.033 0.001 TRP A 669 HIS 0.005 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00195 (17440) covalent geometry : angle 0.47527 (23610) hydrogen bonds : bond 0.02865 ( 542) hydrogen bonds : angle 4.46713 ( 1542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue THR 292 is missing expected H atoms. Skipping. Residue ALA 294 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue ALA 301 is missing expected H atoms. Skipping. Residue SER 451 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue ILE 745 is missing expected H atoms. Skipping. Residue VAL 902 is missing expected H atoms. Skipping. Residue ALA 927 is missing expected H atoms. Skipping. Residue ALA 928 is missing expected H atoms. Skipping. Residue VAL 1013 is missing expected H atoms. Skipping. Residue ALA 1101 is missing expected H atoms. Skipping. Residue LEU 1305 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.822 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: symmetry clash REVERT: A 551 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8212 (mtt90) REVERT: A 762 ARG cc_start: 0.8459 (mtm110) cc_final: 0.7606 (mmp-170) REVERT: A 1027 ASP cc_start: 0.7473 (m-30) cc_final: 0.7112 (m-30) REVERT: A 1214 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: B 551 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8219 (mtt90) REVERT: B 762 ARG cc_start: 0.8450 (mtm110) cc_final: 0.7618 (mmp-170) REVERT: B 1027 ASP cc_start: 0.7496 (m-30) cc_final: 0.7136 (m-30) outliers start: 30 outliers final: 27 residues processed: 211 average time/residue: 0.3584 time to fit residues: 106.9918 Evaluate side-chains 217 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1166 ASN Chi-restraints excluded: chain B residue 1262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 84 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 137 optimal weight: 0.0570 chunk 152 optimal weight: 0.0970 chunk 179 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143297 restraints weight = 54356.915| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.74 r_work: 0.3529 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17440 Z= 0.078 Angle : 0.465 4.799 23610 Z= 0.251 Chirality : 0.038 0.132 2416 Planarity : 0.003 0.052 3164 Dihedral : 3.996 16.861 2392 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.41 % Allowed : 9.52 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2054 helix: 0.24 (1.23), residues: 20 sheet: 1.34 (0.20), residues: 726 loop : -1.27 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 509 TYR 0.008 0.001 TYR B1286 PHE 0.023 0.001 PHE B 271 TRP 0.036 0.001 TRP B 669 HIS 0.005 0.000 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00178 (17440) covalent geometry : angle 0.46508 (23610) hydrogen bonds : bond 0.02637 ( 542) hydrogen bonds : angle 4.30106 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8119.83 seconds wall clock time: 138 minutes 11.68 seconds (8291.68 seconds total)