Starting phenix.real_space_refine on Fri Jan 24 07:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyf_37926/01_2025/8wyf_37926_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.077 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 P 8 5.49 5 S 78 5.16 5 C 13832 2.51 5 N 3460 2.21 5 O 4030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21408 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7895 Classifications: {'peptide': 945} Link IDs: {'PTRANS': 19, 'TRANS': 925} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "C" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Chain: "D" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2195 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.42, per 1000 atoms: 0.67 Number of scatterers: 21408 At special positions: 0 Unit cell: (99.24, 126.531, 180.286, 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 78 16.00 P 8 15.00 O 4030 8.00 N 3460 7.00 C 13832 6.00 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: 5.68 Conformation dependent library (CDL) restraints added in 2.9 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 9 sheets defined 68.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.034A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.762A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.911A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 6.771A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N MET A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.779A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.559A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.089A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.708A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 373' Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 495 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 521 removed outlier: 4.320A pdb=" N ASN A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.512A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.641A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 768 through 788 removed outlier: 3.868A pdb=" N ASP A 788 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 832 through 841 removed outlier: 3.747A pdb=" N ASP A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.526A pdb=" N GLU A 932 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.684A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.817A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 993 through 1004 removed outlier: 4.448A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.025A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.757A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.617A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.560A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.741A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.610A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.725A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 298 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.856A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 495 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.658A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.341A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.630A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.667A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.645A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.506A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.531A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.859A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 961 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 992 Processing helix chain 'B' and resid 993 through 1003 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 47 through 54 removed outlier: 4.044A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.557A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.749A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.676A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.643A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 160' Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 234 removed outlier: 3.637A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 297 removed outlier: 3.955A pdb=" N LEU C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.059A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.563A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 115 through 123 removed outlier: 3.528A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 155 through 161 removed outlier: 4.278A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'E' and resid 95 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.241A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.952A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.167A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 8.575A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.402A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 71 through 72 removed outlier: 7.189A pdb=" N GLU E 38 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU E 33 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN E 40 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE E 31 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE E 44 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL E 27 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 32 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE E 83 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 71 through 72 removed outlier: 10.211A pdb=" N GLU E 115 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE E 44 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) 1170 hydrogen bonds defined for protein. 3366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.81 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3739 1.32 - 1.44: 6037 1.44 - 1.57: 12003 1.57 - 1.69: 15 1.69 - 1.81: 129 Bond restraints: 21923 Sorted by residual: bond pdb=" O3 NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.653 1.566 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4A NAD D1101 " pdb=" N9A NAD D1101 " ideal model delta sigma weight residual 1.367 1.303 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5B NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.638 1.574 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C5A NAD D1101 " pdb=" C6A NAD D1101 " ideal model delta sigma weight residual 1.407 1.468 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 21918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 29431 2.92 - 5.84: 142 5.84 - 8.76: 27 8.76 - 11.68: 9 11.68 - 14.60: 1 Bond angle restraints: 29610 Sorted by residual: angle pdb=" C2B NAD D1101 " pdb=" C1B NAD D1101 " pdb=" N9A NAD D1101 " ideal model delta sigma weight residual 114.24 99.64 14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA GLN C 109 " pdb=" CB GLN C 109 " pdb=" CG GLN C 109 " ideal model delta sigma weight residual 114.10 122.57 -8.47 2.00e+00 2.50e-01 1.80e+01 angle pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" O2B NAD A1101 " ideal model delta sigma weight residual 113.98 102.88 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C2A NAD A1101 " pdb=" N3A NAD A1101 " pdb=" C4A NAD A1101 " ideal model delta sigma weight residual 111.69 122.68 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2A NAD B1101 " pdb=" N3A NAD B1101 " pdb=" C4A NAD B1101 " ideal model delta sigma weight residual 111.69 122.10 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 29605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 10912 18.23 - 36.47: 1666 36.47 - 54.70: 429 54.70 - 72.94: 83 72.94 - 91.17: 48 Dihedral angle restraints: 13138 sinusoidal: 5561 harmonic: 7577 Sorted by residual: dihedral pdb=" CA TYR C 166 " pdb=" C TYR C 166 " pdb=" N LEU C 167 " pdb=" CA LEU C 167 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ILE E 20 " pdb=" C ILE E 20 " pdb=" N ASN E 21 " pdb=" CA ASN E 21 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CG ARG A 165 " pdb=" CD ARG A 165 " pdb=" NE ARG A 165 " pdb=" CZ ARG A 165 " ideal model delta sinusoidal sigma weight residual 90.00 43.22 46.78 2 1.50e+01 4.44e-03 1.13e+01 ... (remaining 13135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2955 0.073 - 0.146: 196 0.146 - 0.219: 6 0.219 - 0.292: 5 0.292 - 0.365: 2 Chirality restraints: 3164 Sorted by residual: chirality pdb=" C4D NAD D1101 " pdb=" C3D NAD D1101 " pdb=" C5D NAD D1101 " pdb=" O4D NAD D1101 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" C4B NAD A1101 " pdb=" O3B NAD A1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" C4B NAD B1101 " pdb=" O3B NAD B1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3161 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 109 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C GLN C 109 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN C 109 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 110 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAD B1101 " -0.025 2.00e-02 2.50e+03 1.15e-02 3.62e+00 pdb=" C2A NAD B1101 " 0.009 2.00e-02 2.50e+03 pdb=" C4A NAD B1101 " 0.004 2.00e-02 2.50e+03 pdb=" C5A NAD B1101 " -0.011 2.00e-02 2.50e+03 pdb=" C6A NAD B1101 " -0.010 2.00e-02 2.50e+03 pdb=" C8A NAD B1101 " 0.015 2.00e-02 2.50e+03 pdb=" N1A NAD B1101 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAD B1101 " 0.008 2.00e-02 2.50e+03 pdb=" N6A NAD B1101 " -0.002 2.00e-02 2.50e+03 pdb=" N7A NAD B1101 " 0.003 2.00e-02 2.50e+03 pdb=" N9A NAD B1101 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 559 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C PHE A 559 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 559 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 560 " -0.010 2.00e-02 2.50e+03 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 255 2.54 - 3.13: 17814 3.13 - 3.72: 35403 3.72 - 4.31: 51399 4.31 - 4.90: 84361 Nonbonded interactions: 189232 Sorted by model distance: nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 1.949 3.040 nonbonded pdb=" OE2 GLU A 685 " pdb=" OG SER A 729 " model vdw 1.972 3.040 nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 1.994 3.040 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 590 " model vdw 1.999 3.040 nonbonded pdb=" OH TYR B 472 " pdb=" OG SER B 546 " model vdw 2.018 3.040 ... (remaining 189227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005 or resid 1101)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005 or resid 1101)) } ncs_group { reference = (chain 'C' and (resid 26 through 297 or resid 1101)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.730 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.004 0.087 21923 Z= 0.244 Angle : 0.551 14.597 29610 Z= 0.257 Chirality : 0.040 0.365 3164 Planarity : 0.002 0.032 3744 Dihedral : 18.783 91.170 8264 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 35.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.37 % Allowed : 29.08 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2517 helix: 1.62 (0.14), residues: 1520 sheet: -1.10 (0.52), residues: 78 loop : -0.08 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.009 0.001 PHE B 699 TYR 0.017 0.001 TYR B 940 ARG 0.003 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: B 504 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5099 (t80) REVERT: D 237 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8419 (mppt) REVERT: E 28 GLU cc_start: 0.7812 (mp0) cc_final: 0.7222 (mt-10) outliers start: 79 outliers final: 72 residues processed: 331 average time/residue: 1.1227 time to fit residues: 434.0598 Evaluate side-chains 331 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 0.0470 chunk 229 optimal weight: 4.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 797 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113383 restraints weight = 31804.277| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.15 r_work: 0.3304 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21923 Z= 0.213 Angle : 0.569 9.403 29610 Z= 0.295 Chirality : 0.042 0.342 3164 Planarity : 0.003 0.041 3744 Dihedral : 10.237 89.002 3145 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.84 % Allowed : 24.35 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2517 helix: 1.33 (0.13), residues: 1540 sheet: -1.35 (0.55), residues: 61 loop : -0.05 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.026 0.001 PHE B 916 TYR 0.022 0.001 TYR B 951 ARG 0.005 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 308 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 61 ARG cc_start: 0.7445 (mtt90) cc_final: 0.6986 (mpp-170) REVERT: A 62 LEU cc_start: 0.7972 (mm) cc_final: 0.7658 (mm) REVERT: A 134 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 370 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6658 (mpt-90) REVERT: A 386 ASN cc_start: 0.7940 (m110) cc_final: 0.7733 (m110) REVERT: A 436 TYR cc_start: 0.8250 (t80) cc_final: 0.7889 (t80) REVERT: A 517 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.7917 (mtm110) REVERT: A 674 ASP cc_start: 0.8404 (p0) cc_final: 0.7876 (t70) REVERT: A 784 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 787 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6130 (tt) REVERT: A 844 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 936 MET cc_start: 0.5198 (mpt) cc_final: 0.4100 (mmt) REVERT: A 961 ASN cc_start: 0.8371 (m110) cc_final: 0.8067 (m110) REVERT: B 69 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 107 PHE cc_start: 0.7526 (m-80) cc_final: 0.7292 (m-80) REVERT: B 188 ASP cc_start: 0.8744 (m-30) cc_final: 0.8425 (m-30) REVERT: B 504 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.5086 (t80) REVERT: B 521 ASN cc_start: 0.7877 (t0) cc_final: 0.7273 (t0) REVERT: B 866 MET cc_start: 0.7511 (mmm) cc_final: 0.7180 (ptt) REVERT: B 881 HIS cc_start: 0.7192 (m170) cc_final: 0.6838 (m-70) REVERT: B 981 ILE cc_start: 0.7765 (mm) cc_final: 0.7400 (mm) REVERT: C 55 ASP cc_start: 0.7703 (t0) cc_final: 0.7482 (t0) REVERT: C 84 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: C 165 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7253 (ptm160) REVERT: C 269 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7081 (pt) REVERT: D 107 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5894 (t80) REVERT: D 124 MET cc_start: 0.7585 (mmm) cc_final: 0.7217 (mmm) REVERT: D 134 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6853 (p90) REVERT: D 237 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8338 (mppt) REVERT: E 26 ASP cc_start: 0.8340 (t0) cc_final: 0.8119 (t0) REVERT: E 28 GLU cc_start: 0.8011 (mp0) cc_final: 0.7354 (mt-10) REVERT: E 37 LYS cc_start: 0.7532 (tptm) cc_final: 0.7052 (ttpt) outliers start: 90 outliers final: 22 residues processed: 367 average time/residue: 1.1347 time to fit residues: 485.3973 Evaluate side-chains 298 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 66 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 609 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 698 GLN B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111887 restraints weight = 31797.528| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.16 r_work: 0.3271 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21923 Z= 0.275 Angle : 0.550 8.730 29610 Z= 0.287 Chirality : 0.042 0.334 3164 Planarity : 0.003 0.046 3744 Dihedral : 9.006 86.070 3054 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.39 % Allowed : 25.37 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2517 helix: 1.15 (0.13), residues: 1551 sheet: -0.99 (0.58), residues: 58 loop : -0.24 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 60 HIS 0.010 0.001 HIS B 349 PHE 0.019 0.002 PHE B 933 TYR 0.015 0.002 TYR B 951 ARG 0.004 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 285 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7994 (mm) cc_final: 0.7683 (mm) REVERT: A 134 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: A 386 ASN cc_start: 0.7992 (m110) cc_final: 0.7736 (m110) REVERT: A 436 TYR cc_start: 0.8429 (t80) cc_final: 0.8133 (t80) REVERT: A 517 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.7949 (mtm110) REVERT: A 784 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7063 (mp0) REVERT: A 787 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.5962 (tt) REVERT: A 844 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 856 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.4873 (t80) REVERT: A 940 TYR cc_start: 0.7273 (t80) cc_final: 0.7072 (t80) REVERT: A 961 ASN cc_start: 0.8466 (m110) cc_final: 0.8189 (m110) REVERT: A 974 LYS cc_start: 0.7991 (pptt) cc_final: 0.7334 (pmmt) REVERT: B 69 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: B 107 PHE cc_start: 0.7451 (m-80) cc_final: 0.7144 (m-10) REVERT: B 188 ASP cc_start: 0.8677 (m-30) cc_final: 0.8349 (m-30) REVERT: B 504 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5071 (t80) REVERT: B 521 ASN cc_start: 0.7918 (t0) cc_final: 0.7284 (t0) REVERT: B 758 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8972 (tp) REVERT: B 866 MET cc_start: 0.7537 (mmm) cc_final: 0.7152 (ptt) REVERT: B 981 ILE cc_start: 0.7820 (mm) cc_final: 0.7534 (mm) REVERT: C 84 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: C 165 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7334 (ptm160) REVERT: C 269 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7118 (pt) REVERT: C 279 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: D 107 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5959 (t80) REVERT: D 134 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7198 (p90) REVERT: D 237 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8400 (mppt) REVERT: E 26 ASP cc_start: 0.8302 (t0) cc_final: 0.8020 (t0) REVERT: E 28 GLU cc_start: 0.8111 (mp0) cc_final: 0.7888 (mp0) REVERT: E 34 SER cc_start: 0.7903 (p) cc_final: 0.7576 (m) REVERT: E 37 LYS cc_start: 0.7533 (tptm) cc_final: 0.7053 (ttpt) outliers start: 103 outliers final: 32 residues processed: 357 average time/residue: 1.1046 time to fit residues: 462.0536 Evaluate side-chains 307 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 765 ASN B 797 ASN D 58 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112929 restraints weight = 32023.599| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.18 r_work: 0.3300 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21923 Z= 0.217 Angle : 0.528 9.837 29610 Z= 0.275 Chirality : 0.041 0.352 3164 Planarity : 0.003 0.043 3744 Dihedral : 8.513 88.461 3048 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.92 % Allowed : 25.46 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2517 helix: 1.23 (0.13), residues: 1543 sheet: -1.01 (0.60), residues: 58 loop : -0.19 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.029 0.001 PHE B 933 TYR 0.016 0.001 TYR A 951 ARG 0.005 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 2.530 Fit side-chains REVERT: A 62 LEU cc_start: 0.7966 (mm) cc_final: 0.7678 (mm) REVERT: A 134 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: A 179 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8472 (tppt) REVERT: A 386 ASN cc_start: 0.7976 (m110) cc_final: 0.7718 (m110) REVERT: A 517 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.7898 (mtm110) REVERT: A 531 MET cc_start: 0.8481 (mmt) cc_final: 0.8246 (mmt) REVERT: A 784 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7056 (mp0) REVERT: A 787 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5919 (tt) REVERT: A 844 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 936 MET cc_start: 0.4965 (mpt) cc_final: 0.3974 (mmt) REVERT: A 961 ASN cc_start: 0.8434 (m110) cc_final: 0.8154 (m110) REVERT: A 974 LYS cc_start: 0.7962 (pptt) cc_final: 0.7297 (pmmt) REVERT: B 17 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: B 69 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: B 107 PHE cc_start: 0.7340 (m-80) cc_final: 0.6971 (m-10) REVERT: B 188 ASP cc_start: 0.8639 (m-30) cc_final: 0.8321 (m-30) REVERT: B 502 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6067 (pmt-80) REVERT: B 504 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.5025 (t80) REVERT: B 521 ASN cc_start: 0.7869 (t0) cc_final: 0.7211 (t0) REVERT: B 758 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8865 (tp) REVERT: B 831 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5967 (pmtt) REVERT: B 866 MET cc_start: 0.7623 (mmm) cc_final: 0.7196 (ptt) REVERT: C 84 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: C 165 ARG cc_start: 0.7545 (ptm160) cc_final: 0.7228 (ptm160) REVERT: C 269 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7073 (pt) REVERT: D 107 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.5909 (t80) REVERT: D 237 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8391 (mppt) REVERT: D 247 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.7421 (ttt-90) REVERT: E 26 ASP cc_start: 0.8239 (t0) cc_final: 0.7898 (t0) REVERT: E 28 GLU cc_start: 0.8183 (mp0) cc_final: 0.7793 (mp0) REVERT: E 34 SER cc_start: 0.7888 (p) cc_final: 0.7599 (m) REVERT: E 37 LYS cc_start: 0.7524 (tptm) cc_final: 0.7051 (ttpt) REVERT: E 80 ASN cc_start: 0.7788 (m110) cc_final: 0.7447 (m-40) outliers start: 92 outliers final: 35 residues processed: 349 average time/residue: 1.1831 time to fit residues: 478.7784 Evaluate side-chains 308 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 219 optimal weight: 0.6980 chunk 221 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 164 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 202 ASN B 349 HIS ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115108 restraints weight = 31656.800| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.18 r_work: 0.3318 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21923 Z= 0.164 Angle : 0.508 10.806 29610 Z= 0.265 Chirality : 0.040 0.344 3164 Planarity : 0.003 0.044 3744 Dihedral : 8.024 86.886 3042 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.75 % Allowed : 25.84 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2517 helix: 1.30 (0.13), residues: 1546 sheet: -0.95 (0.63), residues: 58 loop : -0.12 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.016 0.001 HIS B 881 PHE 0.015 0.001 PHE B 699 TYR 0.014 0.001 TYR B 92 ARG 0.007 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 301 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: A 61 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7314 (mtt180) REVERT: A 62 LEU cc_start: 0.8029 (mm) cc_final: 0.7767 (mm) REVERT: A 134 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 274 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 386 ASN cc_start: 0.8047 (m110) cc_final: 0.7803 (m110) REVERT: A 436 TYR cc_start: 0.8125 (t80) cc_final: 0.7721 (t80) REVERT: A 517 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.7922 (mtm110) REVERT: A 531 MET cc_start: 0.8474 (mmt) cc_final: 0.8251 (mmt) REVERT: A 567 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 674 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7873 (t70) REVERT: A 784 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7032 (mp0) REVERT: A 787 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6061 (tt) REVERT: A 844 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 961 ASN cc_start: 0.8568 (m110) cc_final: 0.8326 (m110) REVERT: A 974 LYS cc_start: 0.7743 (pptt) cc_final: 0.7172 (pmmt) REVERT: B 17 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6521 (tp30) REVERT: B 69 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 188 ASP cc_start: 0.8594 (m-30) cc_final: 0.8261 (m-30) REVERT: B 502 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5969 (pmt-80) REVERT: B 521 ASN cc_start: 0.7867 (t0) cc_final: 0.7201 (t0) REVERT: B 758 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8924 (tp) REVERT: B 831 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6125 (pmtt) REVERT: B 981 ILE cc_start: 0.7873 (mm) cc_final: 0.7579 (mm) REVERT: C 84 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: C 134 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7001 (p90) REVERT: C 165 ARG cc_start: 0.7563 (ptm160) cc_final: 0.7238 (ptm160) REVERT: C 269 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7190 (pt) REVERT: D 107 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.5921 (t80) REVERT: D 237 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8378 (mppt) REVERT: E 26 ASP cc_start: 0.8231 (t0) cc_final: 0.7914 (t0) REVERT: E 28 GLU cc_start: 0.8175 (mp0) cc_final: 0.7915 (mp0) REVERT: E 37 LYS cc_start: 0.7520 (tptm) cc_final: 0.7024 (ttpt) outliers start: 88 outliers final: 31 residues processed: 360 average time/residue: 1.1452 time to fit residues: 481.7279 Evaluate side-chains 314 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 145 optimal weight: 0.4980 chunk 219 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 349 HIS B 881 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114673 restraints weight = 31883.677| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.16 r_work: 0.3310 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21923 Z= 0.186 Angle : 0.517 10.789 29610 Z= 0.269 Chirality : 0.040 0.358 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.775 87.265 3038 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.54 % Allowed : 26.14 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2517 helix: 1.31 (0.13), residues: 1547 sheet: -1.02 (0.63), residues: 58 loop : -0.14 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.019 0.001 PHE B 107 TYR 0.016 0.001 TYR B 92 ARG 0.006 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 285 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: A 62 LEU cc_start: 0.8046 (mm) cc_final: 0.7770 (mm) REVERT: A 386 ASN cc_start: 0.8045 (m110) cc_final: 0.7813 (m110) REVERT: A 517 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.7905 (mtm110) REVERT: A 531 MET cc_start: 0.8493 (mmt) cc_final: 0.8268 (mmt) REVERT: A 567 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 674 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7906 (t70) REVERT: A 784 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7021 (mp0) REVERT: A 787 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6057 (tt) REVERT: A 844 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (mp) REVERT: A 934 ILE cc_start: 0.7471 (pt) cc_final: 0.7249 (pp) REVERT: A 961 ASN cc_start: 0.8579 (m110) cc_final: 0.8340 (m110) REVERT: A 974 LYS cc_start: 0.7728 (pptt) cc_final: 0.7157 (pmmt) REVERT: B 17 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6540 (tp30) REVERT: B 69 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 107 PHE cc_start: 0.7763 (m-80) cc_final: 0.7277 (m-10) REVERT: B 188 ASP cc_start: 0.8608 (m-30) cc_final: 0.8278 (m-30) REVERT: B 502 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6040 (pmt-80) REVERT: B 504 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5163 (t80) REVERT: B 521 ASN cc_start: 0.7901 (t0) cc_final: 0.7238 (t0) REVERT: B 758 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 831 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6154 (pmtt) REVERT: B 866 MET cc_start: 0.7550 (mmm) cc_final: 0.7316 (mmp) REVERT: B 884 LEU cc_start: 0.7869 (tp) cc_final: 0.7327 (tp) REVERT: B 887 GLU cc_start: 0.7801 (pp20) cc_final: 0.7368 (pp20) REVERT: B 981 ILE cc_start: 0.7831 (mm) cc_final: 0.7436 (mm) REVERT: C 84 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: C 119 ASP cc_start: 0.7628 (m-30) cc_final: 0.6848 (p0) REVERT: C 134 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6920 (p90) REVERT: C 165 ARG cc_start: 0.7496 (ptm160) cc_final: 0.7171 (ptm160) REVERT: C 269 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7166 (pt) REVERT: D 107 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.5957 (t80) REVERT: D 227 MET cc_start: 0.8355 (mmp) cc_final: 0.7745 (pp-130) REVERT: D 237 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8385 (mppt) REVERT: D 247 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.7273 (ttt-90) REVERT: E 26 ASP cc_start: 0.8219 (t0) cc_final: 0.7902 (t0) REVERT: E 34 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7628 (m) REVERT: E 37 LYS cc_start: 0.7533 (tptm) cc_final: 0.7045 (ttpt) outliers start: 83 outliers final: 32 residues processed: 343 average time/residue: 1.1196 time to fit residues: 449.0630 Evaluate side-chains 315 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 174 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 182 ASN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115289 restraints weight = 31527.941| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.17 r_work: 0.3308 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21923 Z= 0.195 Angle : 0.524 11.195 29610 Z= 0.271 Chirality : 0.040 0.373 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.546 86.102 3035 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.28 % Allowed : 26.82 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2517 helix: 1.33 (0.13), residues: 1549 sheet: -1.03 (0.63), residues: 58 loop : -0.14 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.017 0.001 PHE B 916 TYR 0.017 0.001 TYR B 92 ARG 0.007 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 279 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7996 (mm) cc_final: 0.7698 (mm) REVERT: A 236 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7217 (mm110) REVERT: A 386 ASN cc_start: 0.8014 (m110) cc_final: 0.7803 (m110) REVERT: A 436 TYR cc_start: 0.8172 (t80) cc_final: 0.7810 (t80) REVERT: A 517 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.7919 (mtm110) REVERT: A 531 MET cc_start: 0.8493 (mmt) cc_final: 0.8290 (mmt) REVERT: A 567 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 578 MET cc_start: 0.6889 (tpp) cc_final: 0.6636 (tmt) REVERT: A 784 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7020 (mp0) REVERT: A 787 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6051 (tt) REVERT: A 844 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7388 (mp) REVERT: A 856 PHE cc_start: 0.5782 (OUTLIER) cc_final: 0.4822 (t80) REVERT: A 936 MET cc_start: 0.4974 (mpp) cc_final: 0.4180 (mmt) REVERT: A 961 ASN cc_start: 0.8565 (m110) cc_final: 0.8324 (m110) REVERT: A 974 LYS cc_start: 0.7725 (pptt) cc_final: 0.7151 (pmmt) REVERT: B 17 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6581 (tp30) REVERT: B 69 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: B 107 PHE cc_start: 0.7582 (m-80) cc_final: 0.7195 (m-10) REVERT: B 188 ASP cc_start: 0.8612 (m-30) cc_final: 0.8286 (m-30) REVERT: B 502 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.5970 (pmt-80) REVERT: B 521 ASN cc_start: 0.7901 (t0) cc_final: 0.7197 (t0) REVERT: B 758 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 831 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.6073 (pmtt) REVERT: B 884 LEU cc_start: 0.7908 (tp) cc_final: 0.7365 (tp) REVERT: B 887 GLU cc_start: 0.7790 (pp20) cc_final: 0.7399 (pp20) REVERT: B 936 MET cc_start: 0.2694 (pmm) cc_final: 0.2258 (pmm) REVERT: B 981 ILE cc_start: 0.7793 (mm) cc_final: 0.7557 (mm) REVERT: C 84 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: C 119 ASP cc_start: 0.7400 (m-30) cc_final: 0.6697 (p0) REVERT: C 134 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.6710 (p90) REVERT: C 165 ARG cc_start: 0.7444 (ptm160) cc_final: 0.7115 (ptm160) REVERT: C 191 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8220 (mp) REVERT: C 269 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7151 (pt) REVERT: D 107 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.5934 (t80) REVERT: D 227 MET cc_start: 0.8339 (mmp) cc_final: 0.7737 (pp-130) REVERT: D 237 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8376 (mppt) REVERT: D 247 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7277 (ttt-90) REVERT: D 262 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7837 (mm-30) REVERT: E 26 ASP cc_start: 0.8243 (t0) cc_final: 0.7926 (t0) REVERT: E 28 GLU cc_start: 0.7858 (mp0) cc_final: 0.7149 (mt-10) REVERT: E 37 LYS cc_start: 0.7514 (tptm) cc_final: 0.7024 (ttpt) outliers start: 77 outliers final: 36 residues processed: 334 average time/residue: 1.1924 time to fit residues: 463.6203 Evaluate side-chains 312 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 246 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 202 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 chunk 158 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 182 ASN B 349 HIS B 797 ASN B 948 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116248 restraints weight = 31591.431| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.17 r_work: 0.3328 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21923 Z= 0.167 Angle : 0.519 11.720 29610 Z= 0.268 Chirality : 0.040 0.380 3164 Planarity : 0.003 0.043 3744 Dihedral : 7.346 86.290 3035 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.45 % Allowed : 26.99 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2517 helix: 1.36 (0.13), residues: 1555 sheet: -1.19 (0.58), residues: 70 loop : -0.09 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.015 0.001 PHE B 699 TYR 0.017 0.001 TYR B 92 ARG 0.007 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7965 (mm) cc_final: 0.7669 (mm) REVERT: A 236 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7201 (mm110) REVERT: A 274 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7883 (tp) REVERT: A 386 ASN cc_start: 0.7924 (m110) cc_final: 0.7719 (m110) REVERT: A 436 TYR cc_start: 0.8201 (t80) cc_final: 0.7788 (t80) REVERT: A 517 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.7918 (mtm110) REVERT: A 567 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8531 (p) REVERT: A 674 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7873 (t70) REVERT: A 784 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7009 (mp0) REVERT: A 787 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.6066 (tt) REVERT: A 844 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7378 (mp) REVERT: A 936 MET cc_start: 0.4964 (mpp) cc_final: 0.4155 (mmt) REVERT: A 961 ASN cc_start: 0.8524 (m110) cc_final: 0.8277 (m110) REVERT: A 974 LYS cc_start: 0.7715 (pptt) cc_final: 0.7154 (pmmt) REVERT: B 17 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6517 (tp30) REVERT: B 69 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 107 PHE cc_start: 0.7405 (m-80) cc_final: 0.7185 (m-80) REVERT: B 188 ASP cc_start: 0.8527 (m-30) cc_final: 0.8194 (m-30) REVERT: B 306 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7102 (t0) REVERT: B 502 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6066 (pmt-80) REVERT: B 504 TYR cc_start: 0.5846 (OUTLIER) cc_final: 0.5133 (t80) REVERT: B 521 ASN cc_start: 0.7888 (t0) cc_final: 0.7167 (t0) REVERT: B 636 PHE cc_start: 0.5004 (m-80) cc_final: 0.4596 (m-80) REVERT: B 722 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (t80) REVERT: B 758 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 831 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6082 (pmtt) REVERT: B 866 MET cc_start: 0.7496 (mmm) cc_final: 0.7208 (mmp) REVERT: B 936 MET cc_start: 0.2684 (pmm) cc_final: 0.2026 (pmm) REVERT: B 981 ILE cc_start: 0.7772 (mm) cc_final: 0.7527 (mm) REVERT: B 1005 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7354 (tt) REVERT: C 84 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: C 119 ASP cc_start: 0.7313 (m-30) cc_final: 0.6636 (p0) REVERT: C 134 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6721 (p90) REVERT: C 165 ARG cc_start: 0.7424 (ptm160) cc_final: 0.7091 (ptm160) REVERT: C 191 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8147 (mp) REVERT: C 269 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7171 (pt) REVERT: D 107 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5911 (t80) REVERT: D 227 MET cc_start: 0.8336 (mmp) cc_final: 0.7740 (pp-130) REVERT: D 237 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8361 (mppt) REVERT: D 247 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.7172 (ttt-90) REVERT: D 262 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7885 (mm-30) REVERT: D 267 ARG cc_start: 0.7345 (mtp180) cc_final: 0.7138 (mtp180) REVERT: E 26 ASP cc_start: 0.8261 (t0) cc_final: 0.7909 (t0) REVERT: E 28 GLU cc_start: 0.7836 (mp0) cc_final: 0.7177 (mt-10) REVERT: E 34 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7641 (m) REVERT: E 37 LYS cc_start: 0.7518 (tptm) cc_final: 0.6998 (ttpt) REVERT: E 41 LYS cc_start: 0.7375 (mttm) cc_final: 0.6812 (mmpt) outliers start: 81 outliers final: 29 residues processed: 342 average time/residue: 1.2262 time to fit residues: 487.1551 Evaluate side-chains 320 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 166 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 349 HIS B 765 ASN B 948 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116143 restraints weight = 31475.123| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.17 r_work: 0.3328 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21923 Z= 0.180 Angle : 0.524 11.638 29610 Z= 0.271 Chirality : 0.040 0.379 3164 Planarity : 0.003 0.041 3744 Dihedral : 7.212 86.752 3035 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.86 % Allowed : 27.72 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2517 helix: 1.40 (0.13), residues: 1553 sheet: -1.16 (0.58), residues: 70 loop : -0.14 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 958 HIS 0.012 0.001 HIS B 349 PHE 0.015 0.001 PHE B 699 TYR 0.018 0.001 TYR B 92 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7982 (mm) cc_final: 0.7672 (mm) REVERT: A 236 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7230 (mm110) REVERT: A 274 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7886 (tp) REVERT: A 436 TYR cc_start: 0.8203 (t80) cc_final: 0.7863 (t80) REVERT: A 517 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.7904 (mtm110) REVERT: A 567 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8549 (p) REVERT: A 578 MET cc_start: 0.6818 (tpp) cc_final: 0.6554 (tmt) REVERT: A 784 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 785 LYS cc_start: 0.7316 (mmtp) cc_final: 0.7091 (mptp) REVERT: A 787 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6074 (tt) REVERT: A 844 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (mp) REVERT: A 936 MET cc_start: 0.5010 (mpp) cc_final: 0.4196 (mmt) REVERT: A 961 ASN cc_start: 0.8532 (m110) cc_final: 0.8289 (m110) REVERT: A 974 LYS cc_start: 0.7695 (pptt) cc_final: 0.7134 (pmmt) REVERT: A 982 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7168 (tt0) REVERT: B 17 GLU cc_start: 0.6772 (pt0) cc_final: 0.6499 (tp30) REVERT: B 69 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: B 107 PHE cc_start: 0.7416 (m-80) cc_final: 0.7214 (m-80) REVERT: B 188 ASP cc_start: 0.8535 (m-30) cc_final: 0.8197 (m-30) REVERT: B 502 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6065 (pmt-80) REVERT: B 504 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5132 (t80) REVERT: B 521 ASN cc_start: 0.7910 (t0) cc_final: 0.7156 (t0) REVERT: B 636 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: B 758 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 831 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6090 (pmtt) REVERT: B 936 MET cc_start: 0.2678 (pmm) cc_final: 0.2029 (pmm) REVERT: B 981 ILE cc_start: 0.7770 (mm) cc_final: 0.7545 (mm) REVERT: B 1005 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7374 (tt) REVERT: C 84 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: C 134 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.6666 (p90) REVERT: C 165 ARG cc_start: 0.7461 (ptm160) cc_final: 0.7133 (ptm160) REVERT: C 191 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8146 (mp) REVERT: C 269 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7278 (pt) REVERT: D 82 ASP cc_start: 0.7450 (m-30) cc_final: 0.7018 (p0) REVERT: D 107 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.5946 (t80) REVERT: D 227 MET cc_start: 0.8360 (mmp) cc_final: 0.7745 (pp-130) REVERT: D 237 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8360 (mppt) REVERT: D 247 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.7196 (ttt-90) REVERT: D 262 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7893 (mm-30) REVERT: D 267 ARG cc_start: 0.7353 (mtp180) cc_final: 0.7143 (mtp180) REVERT: E 26 ASP cc_start: 0.8296 (t0) cc_final: 0.7952 (t0) REVERT: E 28 GLU cc_start: 0.7865 (mp0) cc_final: 0.7214 (mt-10) REVERT: E 34 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7722 (m) REVERT: E 37 LYS cc_start: 0.7530 (tptm) cc_final: 0.6993 (ttpt) REVERT: E 41 LYS cc_start: 0.7378 (mttm) cc_final: 0.6849 (mmpt) outliers start: 67 outliers final: 34 residues processed: 321 average time/residue: 1.2335 time to fit residues: 459.5613 Evaluate side-chains 315 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 636 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 238 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 112 optimal weight: 0.0050 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 349 HIS B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115387 restraints weight = 31989.169| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.21 r_work: 0.3325 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21923 Z= 0.189 Angle : 0.533 11.667 29610 Z= 0.275 Chirality : 0.040 0.381 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.109 86.820 3035 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.77 % Allowed : 28.06 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2517 helix: 1.39 (0.13), residues: 1555 sheet: -1.17 (0.58), residues: 70 loop : -0.15 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 958 HIS 0.012 0.001 HIS B 349 PHE 0.016 0.001 PHE B 699 TYR 0.019 0.001 TYR B 940 ARG 0.008 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7958 (mm) cc_final: 0.7630 (mm) REVERT: A 236 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7263 (mm110) REVERT: A 274 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 295 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7347 (mt-10) REVERT: A 517 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.7911 (mtm110) REVERT: A 567 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 784 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6967 (mp0) REVERT: A 785 LYS cc_start: 0.7317 (mmtp) cc_final: 0.7098 (mptp) REVERT: A 787 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.6046 (tt) REVERT: A 844 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 936 MET cc_start: 0.4952 (mpp) cc_final: 0.4153 (mmt) REVERT: A 961 ASN cc_start: 0.8548 (m110) cc_final: 0.8316 (m110) REVERT: A 974 LYS cc_start: 0.7692 (pptt) cc_final: 0.7115 (pmmt) REVERT: A 982 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7197 (tt0) REVERT: B 17 GLU cc_start: 0.6772 (pt0) cc_final: 0.6493 (tp30) REVERT: B 65 LYS cc_start: 0.8332 (tttm) cc_final: 0.8106 (tttt) REVERT: B 69 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: B 107 PHE cc_start: 0.7446 (m-80) cc_final: 0.7119 (m-80) REVERT: B 181 GLU cc_start: 0.8407 (pp20) cc_final: 0.8194 (pp20) REVERT: B 188 ASP cc_start: 0.8567 (m-30) cc_final: 0.8241 (m-30) REVERT: B 502 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6077 (pmt-80) REVERT: B 504 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5114 (t80) REVERT: B 521 ASN cc_start: 0.7891 (t0) cc_final: 0.7165 (t0) REVERT: B 636 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4392 (m-80) REVERT: B 722 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8838 (t80) REVERT: B 758 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 831 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6141 (pmtt) REVERT: B 866 MET cc_start: 0.7437 (mmm) cc_final: 0.7169 (mmp) REVERT: B 936 MET cc_start: 0.2644 (pmm) cc_final: 0.2230 (pmm) REVERT: B 981 ILE cc_start: 0.7803 (mm) cc_final: 0.7574 (mm) REVERT: B 1005 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 84 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: C 119 ASP cc_start: 0.7292 (m-30) cc_final: 0.6636 (p0) REVERT: C 134 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6599 (p90) REVERT: C 165 ARG cc_start: 0.7452 (ptm160) cc_final: 0.7130 (ptm160) REVERT: C 191 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8180 (mp) REVERT: C 267 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7278 (mtm180) REVERT: C 269 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (pt) REVERT: D 79 TYR cc_start: 0.3365 (m-10) cc_final: 0.3030 (m-10) REVERT: D 82 ASP cc_start: 0.7475 (m-30) cc_final: 0.7051 (p0) REVERT: D 107 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.5891 (t80) REVERT: D 227 MET cc_start: 0.8342 (mmp) cc_final: 0.7757 (pp-130) REVERT: D 237 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8398 (mppt) REVERT: D 247 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.7206 (ttt-90) REVERT: D 262 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7893 (mm-30) REVERT: D 267 ARG cc_start: 0.7390 (mtp180) cc_final: 0.7182 (mtp180) REVERT: E 26 ASP cc_start: 0.8331 (t0) cc_final: 0.7992 (t0) REVERT: E 28 GLU cc_start: 0.7889 (mp0) cc_final: 0.7275 (mt-10) REVERT: E 34 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7728 (m) REVERT: E 37 LYS cc_start: 0.7539 (tptm) cc_final: 0.7000 (ttpt) REVERT: E 41 LYS cc_start: 0.7382 (mttm) cc_final: 0.6809 (mmpt) outliers start: 65 outliers final: 35 residues processed: 324 average time/residue: 1.2200 time to fit residues: 457.3587 Evaluate side-chains 322 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 636 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 205 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 202 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS B 109 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 349 HIS B 765 ASN B 797 ASN B 948 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116203 restraints weight = 32145.849| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.21 r_work: 0.3336 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21923 Z= 0.170 Angle : 0.531 12.265 29610 Z= 0.273 Chirality : 0.040 0.375 3164 Planarity : 0.003 0.043 3744 Dihedral : 6.977 86.649 3033 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.77 % Allowed : 28.10 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2517 helix: 1.42 (0.13), residues: 1554 sheet: -1.16 (0.58), residues: 70 loop : -0.12 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 958 HIS 0.013 0.001 HIS A 810 PHE 0.020 0.001 PHE A 811 TYR 0.018 0.001 TYR B 92 ARG 0.008 0.000 ARG C 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16678.21 seconds wall clock time: 296 minutes 3.10 seconds (17763.10 seconds total)