Starting phenix.real_space_refine on Sun Aug 24 17:01:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyf_37926/08_2025/8wyf_37926_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyf_37926/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wyf_37926/08_2025/8wyf_37926_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyf_37926/08_2025/8wyf_37926_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wyf_37926/08_2025/8wyf_37926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyf_37926/08_2025/8wyf_37926.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.077 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.61, per 1000 atoms: 0.17 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: 1.71 Conformation dependent library (CDL) restraints added in 786.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 3.54 Time building geometry restraints manager: 2.20 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 1101)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1101)) } ncs_group { reference = (chain 'C' and resid 26 through 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: 13.550 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.520 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- 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= 0.183 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 : 35.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 517 TYR 0.017 0.001 TYR B 940 PHE 0.009 0.001 PHE B 699 TRP 0.015 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00382 (21923) covalent geometry : angle 0.55097 (29610) hydrogen bonds : bond 0.13428 ( 1162) hydrogen bonds : angle 5.88463 ( 3366) *********************** 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 : 0.823 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: 0.4454 time to fit residues: 172.1732 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 : 0.772 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** D 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111988 restraints weight = 31856.473| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.15 r_work: 0.3271 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21923 Z= 0.175 Angle : 0.585 9.391 29610 Z= 0.304 Chirality : 0.042 0.332 3164 Planarity : 0.003 0.041 3744 Dihedral : 10.448 88.567 3145 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.01 % Allowed : 24.90 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.16), residues: 2517 helix: 1.28 (0.13), residues: 1536 sheet: -1.36 (0.55), residues: 61 loop : -0.08 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 165 TYR 0.022 0.002 TYR B 951 PHE 0.025 0.002 PHE B 916 TRP 0.017 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00416 (21923) covalent geometry : angle 0.58477 (29610) hydrogen bonds : bond 0.04313 ( 1162) hydrogen bonds : angle 4.89432 ( 3366) *********************** 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 385 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 291 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: A 61 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7050 (mpp-170) REVERT: A 62 LEU cc_start: 0.8050 (mm) cc_final: 0.7753 (mm) REVERT: A 134 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: A 370 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6806 (mpt-90) REVERT: A 436 TYR cc_start: 0.8332 (t80) cc_final: 0.8000 (t80) REVERT: A 517 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.7942 (mtm110) REVERT: A 787 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6182 (tt) REVERT: A 844 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 856 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.4973 (t80) REVERT: A 936 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4122 (mmt) REVERT: A 961 ASN cc_start: 0.8428 (m110) cc_final: 0.8168 (m110) REVERT: B 69 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 107 PHE cc_start: 0.7627 (m-80) cc_final: 0.7409 (m-80) REVERT: B 188 ASP cc_start: 0.8774 (m-30) cc_final: 0.8460 (m-30) REVERT: B 504 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5094 (t80) REVERT: B 521 ASN cc_start: 0.7895 (t0) cc_final: 0.7294 (t0) REVERT: B 881 HIS cc_start: 0.7188 (m170) cc_final: 0.6846 (m-70) REVERT: C 55 ASP cc_start: 0.7708 (t0) cc_final: 0.7486 (t0) REVERT: C 84 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: C 165 ARG cc_start: 0.7700 (ptm160) cc_final: 0.7366 (ptm160) REVERT: C 269 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7117 (pt) REVERT: C 279 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: D 107 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.5969 (t80) REVERT: D 134 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6964 (p90) REVERT: D 237 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8350 (mppt) REVERT: E 28 GLU cc_start: 0.8041 (mp0) cc_final: 0.7370 (mt-10) REVERT: E 37 LYS cc_start: 0.7531 (tptm) cc_final: 0.7050 (ttpt) outliers start: 94 outliers final: 28 residues processed: 354 average time/residue: 0.4865 time to fit residues: 200.4873 Evaluate side-chains 304 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU 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 370 ARG 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 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 936 MET 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 191 LEU 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 729 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 252 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113305 restraints weight = 31896.985| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.16 r_work: 0.3290 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1448 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= 0.139 Angle : 0.526 9.514 29610 Z= 0.274 Chirality : 0.041 0.344 3164 Planarity : 0.003 0.045 3744 Dihedral : 8.999 87.000 3059 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.26 % Allowed : 25.25 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.16), residues: 2517 helix: 1.25 (0.13), residues: 1542 sheet: -0.97 (0.61), residues: 51 loop : -0.15 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 747 TYR 0.015 0.001 TYR A 951 PHE 0.017 0.001 PHE B 933 TRP 0.016 0.001 TRP B 60 HIS 0.011 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00326 (21923) covalent geometry : angle 0.52574 (29610) hydrogen bonds : bond 0.03840 ( 1162) hydrogen bonds : angle 4.67244 ( 3366) *********************** 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 398 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 298 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8036 (mm) cc_final: 0.7739 (mm) REVERT: A 134 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: A 386 ASN cc_start: 0.8003 (m110) cc_final: 0.7760 (m110) REVERT: A 517 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.7901 (mtm110) REVERT: A 784 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7117 (mp0) REVERT: A 787 ILE cc_start: 0.6407 (OUTLIER) cc_final: 0.5993 (tt) REVERT: A 844 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7464 (mp) REVERT: A 961 ASN cc_start: 0.8452 (m110) cc_final: 0.8208 (m110) REVERT: A 974 LYS cc_start: 0.7961 (pptt) cc_final: 0.7311 (pmmt) REVERT: B 69 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: B 107 PHE cc_start: 0.7464 (m-80) cc_final: 0.7146 (m-10) REVERT: B 188 ASP cc_start: 0.8704 (m-30) cc_final: 0.8361 (m-30) REVERT: B 504 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.5079 (t80) REVERT: B 521 ASN cc_start: 0.7914 (t0) cc_final: 0.7257 (t0) REVERT: B 758 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8957 (tp) REVERT: B 866 MET cc_start: 0.7498 (mmm) cc_final: 0.7169 (ptt) REVERT: B 981 ILE cc_start: 0.7878 (mm) cc_final: 0.7582 (mm) REVERT: C 84 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: C 165 ARG cc_start: 0.7635 (ptm160) cc_final: 0.7362 (ptm160) REVERT: C 269 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7151 (pt) REVERT: D 107 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.5970 (t80) REVERT: D 134 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7165 (p90) REVERT: D 237 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8392 (mppt) REVERT: E 26 ASP cc_start: 0.8343 (t0) cc_final: 0.8140 (t0) REVERT: E 28 GLU cc_start: 0.8094 (mp0) cc_final: 0.7894 (mp0) REVERT: E 37 LYS cc_start: 0.7522 (tptm) cc_final: 0.7039 (ttpt) outliers start: 100 outliers final: 26 residues processed: 367 average time/residue: 0.4902 time to fit residues: 210.0295 Evaluate side-chains 297 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER 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 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 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 C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 242 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 698 GLN 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** E 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112729 restraints weight = 31629.664| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.09 r_work: 0.3276 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21923 Z= 0.183 Angle : 0.547 9.299 29610 Z= 0.286 Chirality : 0.042 0.354 3164 Planarity : 0.003 0.043 3744 Dihedral : 8.547 87.477 3046 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.09 % Allowed : 25.54 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2517 helix: 1.12 (0.13), residues: 1550 sheet: -1.02 (0.60), residues: 58 loop : -0.28 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.014 0.002 TYR B 755 PHE 0.030 0.002 PHE B 933 TRP 0.015 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00437 (21923) covalent geometry : angle 0.54709 (29610) hydrogen bonds : bond 0.03995 ( 1162) hydrogen bonds : angle 4.68054 ( 3366) *********************** 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 381 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 285 time to evaluate : 0.934 Fit side-chains REVERT: A 62 LEU cc_start: 0.8036 (mm) cc_final: 0.7734 (mm) REVERT: A 134 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: A 179 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8475 (mptt) REVERT: A 386 ASN cc_start: 0.8044 (m110) cc_final: 0.7783 (m110) REVERT: A 436 TYR cc_start: 0.8356 (t80) cc_final: 0.8060 (t80) REVERT: A 517 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.7955 (mtm110) REVERT: A 531 MET cc_start: 0.8531 (mmt) cc_final: 0.8303 (mmt) REVERT: A 784 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7121 (mp0) REVERT: A 787 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.5973 (tt) REVERT: A 844 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 856 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.5005 (t80) REVERT: A 936 MET cc_start: 0.5006 (OUTLIER) cc_final: 0.3989 (mmt) REVERT: A 961 ASN cc_start: 0.8508 (m110) cc_final: 0.8276 (m110) REVERT: A 974 LYS cc_start: 0.7984 (pptt) cc_final: 0.7321 (pmmt) REVERT: B 17 GLU cc_start: 0.6873 (pt0) cc_final: 0.6617 (tp30) REVERT: B 69 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 107 PHE cc_start: 0.7462 (m-80) cc_final: 0.7129 (m-10) REVERT: B 188 ASP cc_start: 0.8675 (m-30) cc_final: 0.8327 (m-30) REVERT: B 502 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6069 (pmt-80) REVERT: B 504 TYR cc_start: 0.5812 (OUTLIER) cc_final: 0.5033 (t80) REVERT: B 521 ASN cc_start: 0.7941 (t0) cc_final: 0.7287 (t0) REVERT: B 758 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8934 (tp) REVERT: B 831 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6098 (pmtt) REVERT: B 866 MET cc_start: 0.7633 (mmm) cc_final: 0.7261 (ptt) REVERT: B 930 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: C 84 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7417 (m-10) REVERT: C 165 ARG cc_start: 0.7622 (ptm160) cc_final: 0.7309 (ptm160) REVERT: C 269 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7172 (pt) REVERT: C 279 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: D 61 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7220 (mmp-170) REVERT: D 107 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5974 (t80) REVERT: D 134 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7317 (p90) REVERT: D 237 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8427 (mppt) REVERT: D 247 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7372 (ttt-90) REVERT: E 26 ASP cc_start: 0.8344 (t0) cc_final: 0.8107 (t0) REVERT: E 34 SER cc_start: 0.7914 (p) cc_final: 0.7613 (m) REVERT: E 37 LYS cc_start: 0.7537 (tptm) cc_final: 0.7049 (ttpt) outliers start: 96 outliers final: 33 residues processed: 351 average time/residue: 0.5430 time to fit residues: 220.6287 Evaluate side-chains 306 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 856 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 294 ILE 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 927 ASN Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 119 ASP 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 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 238 ASP Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 174 optimal weight: 0.4980 chunk 111 optimal weight: 0.3980 chunk 221 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 349 HIS B 765 ASN B 948 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114486 restraints weight = 31558.445| |-----------------------------------------------------------------------------| r_work (start): 0.3419 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: 0.8189 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21923 Z= 0.117 Angle : 0.509 10.691 29610 Z= 0.266 Chirality : 0.040 0.351 3164 Planarity : 0.003 0.045 3744 Dihedral : 8.115 87.162 3044 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.71 % Allowed : 26.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.16), residues: 2517 helix: 1.26 (0.13), residues: 1546 sheet: -0.93 (0.63), residues: 58 loop : -0.16 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.015 0.001 TYR A 951 PHE 0.016 0.001 PHE B 933 TRP 0.015 0.001 TRP B 60 HIS 0.011 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00267 (21923) covalent geometry : angle 0.50916 (29610) hydrogen bonds : bond 0.03488 ( 1162) hydrogen bonds : angle 4.50523 ( 3366) *********************** 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 382 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 295 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: A 62 LEU cc_start: 0.8042 (mm) cc_final: 0.7778 (mm) REVERT: A 134 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 179 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8535 (tppt) REVERT: A 386 ASN cc_start: 0.8045 (m110) cc_final: 0.7799 (m110) REVERT: A 517 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.7933 (mtm110) REVERT: A 531 MET cc_start: 0.8497 (mmt) cc_final: 0.8250 (mmt) REVERT: A 567 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (p) REVERT: A 674 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7821 (t70) REVERT: A 784 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7106 (mp0) REVERT: A 787 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6010 (tt) REVERT: A 844 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 936 MET cc_start: 0.4753 (mpt) cc_final: 0.3853 (mmt) REVERT: A 961 ASN cc_start: 0.8538 (m110) cc_final: 0.8299 (m110) REVERT: A 974 LYS cc_start: 0.7794 (pptt) cc_final: 0.7191 (pmmt) REVERT: B 17 GLU cc_start: 0.6895 (pt0) cc_final: 0.6581 (tp30) REVERT: B 69 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 188 ASP cc_start: 0.8643 (m-30) cc_final: 0.8321 (m-30) REVERT: B 502 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.5978 (pmt-80) REVERT: B 521 ASN cc_start: 0.7873 (t0) cc_final: 0.7205 (t0) REVERT: B 831 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6115 (pmtt) REVERT: B 930 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: B 981 ILE cc_start: 0.7838 (mm) cc_final: 0.7582 (mm) REVERT: C 84 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: C 119 ASP cc_start: 0.7633 (m-30) cc_final: 0.6858 (p0) REVERT: C 134 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7019 (p90) REVERT: C 165 ARG cc_start: 0.7509 (ptm160) cc_final: 0.7192 (ptm160) REVERT: C 269 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7167 (pt) REVERT: D 107 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.5927 (t80) REVERT: D 134 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7297 (p90) REVERT: D 237 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8388 (mppt) REVERT: D 247 ARG cc_start: 0.7618 (ttt-90) cc_final: 0.7418 (ttt-90) REVERT: D 274 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7838 (tp) REVERT: E 26 ASP cc_start: 0.8252 (t0) cc_final: 0.7921 (t0) REVERT: E 28 GLU cc_start: 0.7851 (mp0) cc_final: 0.7209 (mt-10) REVERT: E 37 LYS cc_start: 0.7544 (tptm) cc_final: 0.7039 (ttpt) outliers start: 87 outliers final: 26 residues processed: 351 average time/residue: 0.5050 time to fit residues: 206.3992 Evaluate side-chains 308 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 232 VAL 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 814 ASN 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 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 801 SER Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR 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 274 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE 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 56 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113561 restraints weight = 31669.412| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.10 r_work: 0.3284 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21923 Z= 0.174 Angle : 0.546 10.155 29610 Z= 0.284 Chirality : 0.041 0.368 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.888 86.133 3038 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.05 % Allowed : 26.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 2517 helix: 1.20 (0.13), residues: 1539 sheet: -1.07 (0.61), residues: 58 loop : -0.21 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.018 0.001 TYR B 92 PHE 0.018 0.002 PHE B 699 TRP 0.014 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00417 (21923) covalent geometry : angle 0.54632 (29610) hydrogen bonds : bond 0.03768 ( 1162) hydrogen bonds : angle 4.59785 ( 3366) *********************** 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 375 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 280 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8066 (mm) cc_final: 0.7659 (mm) REVERT: A 107 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6637 (t80) REVERT: A 134 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 179 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8564 (tppt) REVERT: A 236 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7246 (mm110) REVERT: A 386 ASN cc_start: 0.8081 (m110) cc_final: 0.7815 (m110) REVERT: A 436 TYR cc_start: 0.8293 (t80) cc_final: 0.8010 (t80) REVERT: A 517 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.7914 (mtm110) REVERT: A 531 MET cc_start: 0.8515 (mmt) cc_final: 0.8252 (mmt) REVERT: A 567 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 774 ILE cc_start: 0.7567 (mt) cc_final: 0.7334 (mm) REVERT: A 784 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 787 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.5989 (tt) REVERT: A 844 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 856 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4783 (t80) REVERT: A 961 ASN cc_start: 0.8535 (m110) cc_final: 0.8290 (m110) REVERT: A 974 LYS cc_start: 0.7915 (pptt) cc_final: 0.7267 (pmmt) REVERT: B 17 GLU cc_start: 0.6960 (pt0) cc_final: 0.6642 (tp30) REVERT: B 188 ASP cc_start: 0.8645 (m-30) cc_final: 0.8328 (m-30) REVERT: B 502 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6081 (pmt-80) REVERT: B 504 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5228 (t80) REVERT: B 521 ASN cc_start: 0.7912 (t0) cc_final: 0.7236 (t0) REVERT: B 758 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 831 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6091 (pmtt) REVERT: B 884 LEU cc_start: 0.7879 (tp) cc_final: 0.7325 (tp) REVERT: B 887 GLU cc_start: 0.7835 (pp20) cc_final: 0.7425 (pp20) REVERT: B 981 ILE cc_start: 0.7866 (mm) cc_final: 0.7502 (mm) REVERT: C 84 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7412 (m-10) REVERT: C 119 ASP cc_start: 0.7641 (m-30) cc_final: 0.6880 (p0) REVERT: C 134 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6865 (p90) REVERT: C 165 ARG cc_start: 0.7580 (ptm160) cc_final: 0.7281 (ptm160) REVERT: C 269 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7185 (pt) REVERT: D 61 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7173 (mmp-170) REVERT: D 107 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.5929 (t80) REVERT: D 227 MET cc_start: 0.8336 (mmp) cc_final: 0.7750 (pp-130) REVERT: D 237 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8416 (mppt) REVERT: D 274 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7826 (tp) REVERT: E 26 ASP cc_start: 0.8286 (t0) cc_final: 0.7962 (t0) REVERT: E 28 GLU cc_start: 0.7918 (mp0) cc_final: 0.7256 (mt-10) REVERT: E 34 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7642 (m) REVERT: E 37 LYS cc_start: 0.7508 (tptm) cc_final: 0.7044 (ttpt) outliers start: 95 outliers final: 34 residues processed: 348 average time/residue: 0.4931 time to fit residues: 199.5693 Evaluate side-chains 315 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 VAL 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 856 PHE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 70 LEU 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 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 927 ASN Chi-restraints excluded: chain C residue 84 TYR 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 D residue 212 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 34 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 242 optimal weight: 0.2980 chunk 117 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 182 ASN B 349 HIS B 797 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 = 0.3846 r_free = 0.3846 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115004 restraints weight = 31650.036| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.17 r_work: 0.3303 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2003 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= 0.125 Angle : 0.525 10.992 29610 Z= 0.273 Chirality : 0.040 0.366 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.613 85.921 3038 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.24 % Allowed : 27.38 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.16), residues: 2517 helix: 1.27 (0.13), residues: 1546 sheet: -1.03 (0.62), residues: 58 loop : -0.17 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 61 TYR 0.016 0.001 TYR B 92 PHE 0.016 0.001 PHE B 916 TRP 0.013 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00292 (21923) covalent geometry : angle 0.52483 (29610) hydrogen bonds : bond 0.03481 ( 1162) hydrogen bonds : angle 4.48981 ( 3366) *********************** 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 359 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 283 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8016 (mm) cc_final: 0.7735 (mm) REVERT: A 134 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: A 179 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8539 (tppt) REVERT: A 236 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7238 (mm110) REVERT: A 386 ASN cc_start: 0.8007 (m110) cc_final: 0.7803 (m110) REVERT: A 517 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.7911 (mtm110) REVERT: A 531 MET cc_start: 0.8511 (mmt) cc_final: 0.8257 (mmt) REVERT: A 567 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8550 (p) REVERT: A 578 MET cc_start: 0.6832 (tpp) cc_final: 0.6573 (tmt) REVERT: A 674 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7866 (t70) REVERT: A 784 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6971 (mp0) REVERT: A 787 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.6031 (tt) REVERT: A 844 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7409 (mp) REVERT: A 961 ASN cc_start: 0.8554 (m110) cc_final: 0.8308 (m110) REVERT: A 974 LYS cc_start: 0.7835 (pptt) cc_final: 0.7224 (pmmt) REVERT: B 17 GLU cc_start: 0.6876 (pt0) cc_final: 0.6568 (tp30) REVERT: B 83 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 188 ASP cc_start: 0.8611 (m-30) cc_final: 0.8288 (m-30) REVERT: B 306 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7095 (t0) REVERT: B 502 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6045 (pmt-80) REVERT: B 504 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.5162 (t80) REVERT: B 521 ASN cc_start: 0.7888 (t0) cc_final: 0.7186 (t0) REVERT: B 636 PHE cc_start: 0.5076 (m-80) cc_final: 0.4667 (m-80) REVERT: B 831 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6137 (pmtt) REVERT: B 981 ILE cc_start: 0.7812 (mm) cc_final: 0.7588 (mm) REVERT: C 84 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7330 (m-10) REVERT: C 119 ASP cc_start: 0.7422 (m-30) cc_final: 0.6711 (p0) REVERT: C 134 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6794 (p90) REVERT: C 165 ARG cc_start: 0.7456 (ptm160) cc_final: 0.7149 (ptm160) REVERT: C 269 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7146 (pt) REVERT: D 61 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7113 (mmp-170) REVERT: D 107 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.5947 (t80) REVERT: D 227 MET cc_start: 0.8349 (mmp) cc_final: 0.7740 (pp-130) REVERT: D 237 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8390 (mppt) REVERT: D 247 ARG cc_start: 0.7488 (ttt-90) cc_final: 0.7259 (ttt-90) REVERT: E 26 ASP cc_start: 0.8290 (t0) cc_final: 0.7940 (t0) REVERT: E 28 GLU cc_start: 0.7929 (mp0) cc_final: 0.7666 (mp0) REVERT: E 34 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7681 (m) REVERT: E 37 LYS cc_start: 0.7519 (tptm) cc_final: 0.7030 (ttpt) outliers start: 76 outliers final: 33 residues processed: 335 average time/residue: 0.4658 time to fit residues: 182.8391 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 : 0.904 ------------------------------------------------------------------------------- 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 236 GLN 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 814 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 106 ASP 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 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 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 238 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 53 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 239 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 182 ASN B 349 HIS B 765 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114135 restraints weight = 31712.543| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.17 r_work: 0.3308 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2050 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= 0.133 Angle : 0.532 11.080 29610 Z= 0.277 Chirality : 0.040 0.368 3164 Planarity : 0.003 0.043 3744 Dihedral : 7.477 86.465 3037 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.24 % Allowed : 27.76 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2517 helix: 1.24 (0.13), residues: 1553 sheet: -1.19 (0.57), residues: 70 loop : -0.22 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 61 TYR 0.018 0.001 TYR B 92 PHE 0.016 0.001 PHE B 699 TRP 0.015 0.002 TRP B 958 HIS 0.012 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00314 (21923) covalent geometry : angle 0.53250 (29610) hydrogen bonds : bond 0.03506 ( 1162) hydrogen bonds : angle 4.49052 ( 3366) *********************** 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 355 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8052 (mm) cc_final: 0.7765 (mm) REVERT: A 134 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: A 179 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8539 (tppt) REVERT: A 236 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7261 (mm110) REVERT: A 274 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7887 (tp) REVERT: A 295 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7405 (mt-10) REVERT: A 386 ASN cc_start: 0.7965 (m110) cc_final: 0.7741 (m110) REVERT: A 436 TYR cc_start: 0.8139 (t80) cc_final: 0.7841 (t80) REVERT: A 517 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.7938 (mtm110) REVERT: A 531 MET cc_start: 0.8518 (mmt) cc_final: 0.8261 (mmt) REVERT: A 567 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 674 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7857 (t70) REVERT: A 714 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.9105 (p) REVERT: A 774 ILE cc_start: 0.7526 (mt) cc_final: 0.7298 (mm) REVERT: A 784 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6991 (mp0) REVERT: A 787 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6044 (tt) REVERT: A 844 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7435 (mp) REVERT: A 936 MET cc_start: 0.4986 (mpp) cc_final: 0.4241 (mmt) REVERT: A 961 ASN cc_start: 0.8579 (m110) cc_final: 0.8347 (m110) REVERT: A 974 LYS cc_start: 0.7839 (pptt) cc_final: 0.7227 (pmmt) REVERT: B 17 GLU cc_start: 0.6952 (pt0) cc_final: 0.6596 (tp30) REVERT: B 181 GLU cc_start: 0.8118 (pp20) cc_final: 0.7877 (pp20) REVERT: B 188 ASP cc_start: 0.8623 (m-30) cc_final: 0.8293 (m-30) REVERT: B 306 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6866 (t0) REVERT: B 502 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6002 (pmt-80) REVERT: B 521 ASN cc_start: 0.7912 (t0) cc_final: 0.7211 (t0) REVERT: B 636 PHE cc_start: 0.5157 (m-80) cc_final: 0.4506 (m-80) REVERT: B 758 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8948 (tp) REVERT: B 831 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6156 (pmtt) REVERT: C 84 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: C 119 ASP cc_start: 0.7341 (m-30) cc_final: 0.6672 (p0) REVERT: C 134 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6708 (p90) REVERT: C 165 ARG cc_start: 0.7482 (ptm160) cc_final: 0.7184 (ptm160) REVERT: C 269 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7196 (pt) REVERT: D 61 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7121 (mmp-170) REVERT: D 107 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.5913 (t80) REVERT: D 227 MET cc_start: 0.8355 (mmp) cc_final: 0.7749 (pp-130) REVERT: D 237 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8397 (mppt) REVERT: D 247 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.7255 (ttt-90) REVERT: E 26 ASP cc_start: 0.8306 (t0) cc_final: 0.7959 (t0) REVERT: E 28 GLU cc_start: 0.7909 (mp0) cc_final: 0.7643 (mp0) REVERT: E 34 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7651 (m) REVERT: E 37 LYS cc_start: 0.7520 (tptm) cc_final: 0.7002 (ttpt) outliers start: 76 outliers final: 33 residues processed: 335 average time/residue: 0.4783 time to fit residues: 186.5805 Evaluate side-chains 315 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain A residue 273 SER 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 714 SER 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 814 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 106 ASP 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 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 1005 ILE 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 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 112 ILE 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 242 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 349 HIS B 765 ASN B 797 ASN B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113849 restraints weight = 31808.916| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.17 r_work: 0.3304 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2078 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= 0.140 Angle : 0.544 11.164 29610 Z= 0.282 Chirality : 0.041 0.372 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.348 86.542 3035 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.99 % Allowed : 28.02 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2517 helix: 1.23 (0.13), residues: 1553 sheet: -1.03 (0.61), residues: 58 loop : -0.24 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 61 TYR 0.019 0.001 TYR B 92 PHE 0.019 0.001 PHE B 933 TRP 0.018 0.002 TRP B 958 HIS 0.012 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00331 (21923) covalent geometry : angle 0.54367 (29610) hydrogen bonds : bond 0.03537 ( 1162) hydrogen bonds : angle 4.49644 ( 3366) *********************** 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 345 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 275 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8035 (mm) cc_final: 0.7748 (mm) REVERT: A 134 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.5895 (m-80) REVERT: A 179 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8536 (tppt) REVERT: A 236 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7283 (mm110) REVERT: A 274 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 295 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7361 (mt-10) REVERT: A 386 ASN cc_start: 0.7947 (m110) cc_final: 0.7723 (m110) REVERT: A 436 TYR cc_start: 0.8253 (t80) cc_final: 0.7945 (t80) REVERT: A 517 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.7934 (mtm110) REVERT: A 531 MET cc_start: 0.8507 (mmt) cc_final: 0.8231 (mmt) REVERT: A 567 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 714 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9087 (p) REVERT: A 774 ILE cc_start: 0.7538 (mt) cc_final: 0.7312 (mm) REVERT: A 784 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6990 (mp0) REVERT: A 787 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6042 (tt) REVERT: A 844 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 936 MET cc_start: 0.5018 (mpp) cc_final: 0.4189 (mmt) REVERT: A 961 ASN cc_start: 0.8590 (m110) cc_final: 0.8356 (m110) REVERT: A 974 LYS cc_start: 0.7823 (pptt) cc_final: 0.7200 (pmmt) REVERT: B 17 GLU cc_start: 0.6928 (pt0) cc_final: 0.6573 (tp30) REVERT: B 181 GLU cc_start: 0.8106 (pp20) cc_final: 0.7835 (pp20) REVERT: B 188 ASP cc_start: 0.8583 (m-30) cc_final: 0.8249 (m-30) REVERT: B 306 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6855 (t0) REVERT: B 502 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6104 (pmt-80) REVERT: B 504 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5142 (t80) REVERT: B 521 ASN cc_start: 0.7920 (t0) cc_final: 0.7193 (t0) REVERT: B 758 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 831 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6149 (pmtt) REVERT: B 936 MET cc_start: 0.2707 (pmm) cc_final: 0.2268 (pmm) REVERT: C 84 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: C 119 ASP cc_start: 0.7558 (m-30) cc_final: 0.6813 (p0) REVERT: C 134 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6683 (p90) REVERT: C 165 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7267 (ptm160) REVERT: C 191 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 269 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7231 (pt) REVERT: D 61 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7103 (mmp-170) REVERT: D 82 ASP cc_start: 0.7477 (m-30) cc_final: 0.7060 (p0) REVERT: D 107 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.5978 (t80) REVERT: D 181 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: D 227 MET cc_start: 0.8344 (mmp) cc_final: 0.7734 (pp-130) REVERT: D 237 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8392 (mppt) REVERT: D 247 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.7260 (ttt-90) REVERT: E 26 ASP cc_start: 0.8328 (t0) cc_final: 0.7977 (t0) REVERT: E 34 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7658 (m) REVERT: E 37 LYS cc_start: 0.7532 (tptm) cc_final: 0.7007 (ttpt) REVERT: E 41 LYS cc_start: 0.7334 (mttm) cc_final: 0.6723 (mmpt) outliers start: 70 outliers final: 37 residues processed: 324 average time/residue: 0.4622 time to fit residues: 173.7120 Evaluate side-chains 324 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 VAL 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 714 SER 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 814 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 106 ASP 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 673 ILE 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 1005 ILE 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 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 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 34 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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** D 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115346 restraints weight = 31869.851| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.22 r_work: 0.3329 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21923 Z= 0.123 Angle : 0.542 11.564 29610 Z= 0.280 Chirality : 0.040 0.371 3164 Planarity : 0.003 0.043 3744 Dihedral : 7.231 86.474 3035 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.73 % Allowed : 28.32 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2517 helix: 1.26 (0.13), residues: 1554 sheet: -1.20 (0.57), residues: 70 loop : -0.21 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 61 TYR 0.026 0.001 TYR B 940 PHE 0.020 0.001 PHE B 933 TRP 0.020 0.002 TRP B 958 HIS 0.012 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00288 (21923) covalent geometry : angle 0.54247 (29610) hydrogen bonds : bond 0.03441 ( 1162) hydrogen bonds : angle 4.46354 ( 3366) ********************** 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 337 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7987 (mm) cc_final: 0.7687 (mm) REVERT: A 134 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.5912 (m-80) REVERT: A 236 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7283 (mm110) REVERT: A 274 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7918 (tp) REVERT: A 295 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7342 (mt-10) REVERT: A 339 HIS cc_start: 0.8010 (m90) cc_final: 0.7635 (m90) REVERT: A 386 ASN cc_start: 0.7933 (m110) cc_final: 0.7724 (m110) REVERT: A 436 TYR cc_start: 0.8229 (t80) cc_final: 0.7863 (t80) REVERT: A 517 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.7939 (mtm110) REVERT: A 531 MET cc_start: 0.8490 (mmt) cc_final: 0.8192 (mmt) REVERT: A 567 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 674 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7864 (t70) REVERT: A 774 ILE cc_start: 0.7544 (mt) cc_final: 0.7299 (mm) REVERT: A 784 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6971 (mp0) REVERT: A 787 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6025 (tt) REVERT: A 844 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7435 (mp) REVERT: A 936 MET cc_start: 0.4929 (mpp) cc_final: 0.4160 (mmt) REVERT: A 961 ASN cc_start: 0.8559 (m110) cc_final: 0.8324 (m110) REVERT: A 974 LYS cc_start: 0.7685 (pptt) cc_final: 0.7094 (pmmt) REVERT: B 17 GLU cc_start: 0.6850 (pt0) cc_final: 0.6553 (tp30) REVERT: B 181 GLU cc_start: 0.8114 (pp20) cc_final: 0.7863 (pp20) REVERT: B 188 ASP cc_start: 0.8568 (m-30) cc_final: 0.8228 (m-30) REVERT: B 306 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6823 (t0) REVERT: B 502 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6102 (pmt-80) REVERT: B 504 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.5110 (t80) REVERT: B 521 ASN cc_start: 0.7906 (t0) cc_final: 0.7162 (t0) REVERT: B 758 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 831 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6093 (pmtt) REVERT: B 866 MET cc_start: 0.7367 (mmm) cc_final: 0.7117 (mmp) REVERT: B 936 MET cc_start: 0.2640 (pmm) cc_final: 0.2215 (pmm) REVERT: C 84 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: C 119 ASP cc_start: 0.7366 (m-30) cc_final: 0.6676 (p0) REVERT: C 134 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.6635 (p90) REVERT: C 165 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7156 (ptm160) REVERT: C 267 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7287 (mtm180) REVERT: C 269 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7199 (pt) REVERT: D 61 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7004 (mmp-170) REVERT: D 82 ASP cc_start: 0.7499 (m-30) cc_final: 0.7073 (p0) REVERT: D 107 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.5887 (t80) REVERT: D 181 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: D 227 MET cc_start: 0.8343 (mmp) cc_final: 0.7741 (pp-130) REVERT: D 237 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8414 (mppt) REVERT: D 247 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.7145 (ttt-90) REVERT: E 26 ASP cc_start: 0.8322 (t0) cc_final: 0.7977 (t0) REVERT: E 34 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7655 (m) REVERT: E 37 LYS cc_start: 0.7565 (tptm) cc_final: 0.7048 (ttpt) outliers start: 64 outliers final: 33 residues processed: 319 average time/residue: 0.4642 time to fit residues: 171.6985 Evaluate side-chains 315 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 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 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 106 ASP 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 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 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 160 ASN 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 181 GLU 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 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 173 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.0020 chunk 205 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 0.0030 chunk 212 optimal weight: 3.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 349 HIS B 765 ASN B 797 ASN B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.149003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115804 restraints weight = 32018.418| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.24 r_work: 0.3341 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2295 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= 0.116 Angle : 0.534 11.435 29610 Z= 0.276 Chirality : 0.040 0.366 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.096 86.451 3035 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.69 % Allowed : 28.44 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2517 helix: 1.34 (0.13), residues: 1547 sheet: -1.02 (0.62), residues: 60 loop : -0.16 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 61 TYR 0.019 0.001 TYR B 92 PHE 0.015 0.001 PHE B 699 TRP 0.020 0.001 TRP B 958 HIS 0.012 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00268 (21923) covalent geometry : angle 0.53363 (29610) hydrogen bonds : bond 0.03381 ( 1162) hydrogen bonds : angle 4.42547 ( 3366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7842.41 seconds wall clock time: 134 minutes 33.84 seconds (8073.84 seconds total)