Starting phenix.real_space_refine on Tue Jul 23 07:00:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/07_2024/8wyf_37926_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 78 5.16 5 C 13832 2.51 5 N 3460 2.21 5 O 4030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21408 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7895 Classifications: {'peptide': 945} Link IDs: {'PTRANS': 19, 'TRANS': 925} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "C" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Chain: "D" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2195 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.45, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 3.5 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 9 sheets defined 68.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 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: 8.42 Time building geometry restraints manager: 9.40 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: 93.48 - 102.08: 61 102.08 - 110.67: 6533 110.67 - 119.26: 11237 119.26 - 127.85: 11617 127.85 - 136.44: 162 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 2.440 nonbonded pdb=" OE2 GLU A 685 " pdb=" OG SER A 729 " model vdw 1.972 2.440 nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 1.994 2.440 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 590 " model vdw 1.999 2.440 nonbonded pdb=" OH TYR B 472 " pdb=" OG SER B 546 " model vdw 2.018 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005 or resid 1101)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005 or resid 1101)) } ncs_group { reference = (chain 'C' and (resid 26 through 297 or resid 1101)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 60.430 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21923 Z= 0.244 Angle : 0.551 14.597 29610 Z= 0.257 Chirality : 0.040 0.365 3164 Planarity : 0.002 0.032 3744 Dihedral : 18.783 91.170 8264 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 35.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.37 % Allowed : 29.08 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2517 helix: 1.62 (0.14), residues: 1520 sheet: -1.10 (0.52), residues: 78 loop : -0.08 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.009 0.001 PHE B 699 TYR 0.017 0.001 TYR B 940 ARG 0.003 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 262 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: B 504 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5099 (t80) REVERT: D 237 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8419 (mppt) REVERT: E 28 GLU cc_start: 0.7812 (mp0) cc_final: 0.7222 (mt-10) outliers start: 79 outliers final: 72 residues processed: 331 average time/residue: 1.0766 time to fit residues: 417.5264 Evaluate side-chains 331 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 258 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 147 optimal weight: 0.0070 chunk 229 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 797 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21923 Z= 0.200 Angle : 0.543 9.227 29610 Z= 0.281 Chirality : 0.041 0.308 3164 Planarity : 0.003 0.040 3744 Dihedral : 10.352 86.784 3145 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.18 % Allowed : 25.42 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2517 helix: 1.46 (0.13), residues: 1534 sheet: -1.15 (0.54), residues: 71 loop : -0.03 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.024 0.001 PHE B 916 TYR 0.020 0.001 TYR B 951 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 292 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7414 (mtt90) cc_final: 0.6975 (mpp-170) REVERT: A 62 LEU cc_start: 0.8100 (mm) cc_final: 0.7798 (mm) REVERT: A 134 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: A 370 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6618 (mmt90) REVERT: A 436 TYR cc_start: 0.8063 (t80) cc_final: 0.7762 (t80) REVERT: A 517 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.7926 (mtm110) REVERT: A 674 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7870 (t70) REVERT: A 784 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 787 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6186 (tt) REVERT: A 844 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 945 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6552 (p0) REVERT: A 961 ASN cc_start: 0.8218 (m110) cc_final: 0.7967 (m110) REVERT: B 54 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 69 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: B 107 PHE cc_start: 0.7554 (m-80) cc_final: 0.7292 (m-80) REVERT: B 504 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.5059 (t80) REVERT: B 521 ASN cc_start: 0.7593 (t0) cc_final: 0.6933 (t0) REVERT: B 809 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (tppt) REVERT: B 866 MET cc_start: 0.7490 (mmm) cc_final: 0.7185 (ptt) REVERT: B 936 MET cc_start: 0.3624 (pmm) cc_final: 0.3353 (pmm) REVERT: B 981 ILE cc_start: 0.7837 (mm) cc_final: 0.7484 (mm) REVERT: C 55 ASP cc_start: 0.7405 (t0) cc_final: 0.7188 (t0) REVERT: C 84 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: C 165 ARG cc_start: 0.7585 (ptm160) cc_final: 0.7210 (ptm160) REVERT: C 269 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7077 (pt) REVERT: D 107 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.5995 (t80) REVERT: D 124 MET cc_start: 0.7529 (mmm) cc_final: 0.7201 (mmm) REVERT: D 134 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7003 (p90) REVERT: D 237 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8402 (mppt) REVERT: E 26 ASP cc_start: 0.8325 (t0) cc_final: 0.8106 (t0) REVERT: E 28 GLU cc_start: 0.7879 (mp0) cc_final: 0.7286 (mt-10) REVERT: E 37 LYS cc_start: 0.7511 (tptm) cc_final: 0.7059 (ttpt) outliers start: 98 outliers final: 30 residues processed: 361 average time/residue: 1.0662 time to fit residues: 450.7994 Evaluate side-chains 303 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 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 874 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 204 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 184 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 765 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21923 Z= 0.164 Angle : 0.495 9.297 29610 Z= 0.257 Chirality : 0.039 0.320 3164 Planarity : 0.003 0.044 3744 Dihedral : 8.885 89.013 3068 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.71 % Allowed : 26.35 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2517 helix: 1.44 (0.13), residues: 1544 sheet: -0.61 (0.64), residues: 51 loop : -0.02 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.018 0.001 PHE B 933 TYR 0.015 0.001 TYR A 951 ARG 0.005 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 298 time to evaluate : 2.626 Fit side-chains REVERT: A 62 LEU cc_start: 0.8097 (mm) cc_final: 0.7842 (mm) REVERT: A 134 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 386 ASN cc_start: 0.7944 (m110) cc_final: 0.7715 (m110) REVERT: A 436 TYR cc_start: 0.8053 (t80) cc_final: 0.7741 (t80) REVERT: A 517 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.7987 (mtm110) REVERT: A 674 ASP cc_start: 0.8349 (p0) cc_final: 0.7925 (t70) REVERT: A 784 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7094 (mp0) REVERT: A 787 ILE cc_start: 0.6460 (OUTLIER) cc_final: 0.6118 (tt) REVERT: A 844 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 856 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4992 (t80) REVERT: A 961 ASN cc_start: 0.8247 (m110) cc_final: 0.8011 (m110) REVERT: A 974 LYS cc_start: 0.7860 (pptt) cc_final: 0.7258 (pmmt) REVERT: B 17 GLU cc_start: 0.6787 (pt0) cc_final: 0.6552 (tp30) REVERT: B 54 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8105 (m) REVERT: B 69 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 107 PHE cc_start: 0.7521 (m-80) cc_final: 0.7265 (m-10) REVERT: B 181 GLU cc_start: 0.8167 (pp20) cc_final: 0.7922 (pp20) REVERT: B 188 ASP cc_start: 0.8573 (m-30) cc_final: 0.8274 (m-30) REVERT: B 521 ASN cc_start: 0.7650 (t0) cc_final: 0.6969 (t0) REVERT: B 758 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8951 (tp) REVERT: B 809 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7727 (tppt) REVERT: B 866 MET cc_start: 0.7540 (mmm) cc_final: 0.7195 (ptt) REVERT: B 981 ILE cc_start: 0.7844 (mm) cc_final: 0.7619 (mm) REVERT: C 84 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: C 269 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7084 (pt) REVERT: D 61 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7274 (mmp-170) REVERT: D 107 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.5976 (t80) REVERT: D 134 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6918 (p90) REVERT: D 237 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8414 (mppt) REVERT: E 26 ASP cc_start: 0.8321 (t0) cc_final: 0.8051 (t0) REVERT: E 37 LYS cc_start: 0.7533 (tptm) cc_final: 0.7059 (ttpt) outliers start: 87 outliers final: 26 residues processed: 357 average time/residue: 1.0680 time to fit residues: 446.0582 Evaluate side-chains 306 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 2.581 ------------------------------------------------------------------------------- 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 140 THR 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 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 848 ASN Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 54 SER 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER 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 809 LYS Chi-restraints excluded: chain B residue 914 SER 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 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 11 THR 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 227 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS C 224 ASN D 58 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21923 Z= 0.235 Angle : 0.519 9.020 29610 Z= 0.270 Chirality : 0.040 0.332 3164 Planarity : 0.003 0.044 3744 Dihedral : 8.273 88.442 3044 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.14 % Allowed : 26.70 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2517 helix: 1.30 (0.13), residues: 1555 sheet: -0.61 (0.62), residues: 58 loop : -0.15 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.017 0.001 PHE B 933 TYR 0.017 0.001 TYR A 709 ARG 0.006 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 277 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7078 (mpp-170) REVERT: A 62 LEU cc_start: 0.8089 (mm) cc_final: 0.7797 (mm) REVERT: A 134 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: A 386 ASN cc_start: 0.7961 (m110) cc_final: 0.7745 (m110) REVERT: A 436 TYR cc_start: 0.8328 (t80) cc_final: 0.8016 (t80) REVERT: A 517 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.7953 (mtm110) REVERT: A 674 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7886 (t70) REVERT: A 784 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7110 (mp0) REVERT: A 787 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6065 (tt) REVERT: A 844 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 856 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4983 (t80) REVERT: A 961 ASN cc_start: 0.8300 (m110) cc_final: 0.8059 (m110) REVERT: A 974 LYS cc_start: 0.7872 (pptt) cc_final: 0.7259 (pmmt) REVERT: B 17 GLU cc_start: 0.6847 (pt0) cc_final: 0.6600 (tp30) REVERT: B 54 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8185 (m) REVERT: B 69 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: B 188 ASP cc_start: 0.8555 (m-30) cc_final: 0.8258 (m-30) REVERT: B 502 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6077 (pmt-80) REVERT: B 504 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5068 (t80) REVERT: B 521 ASN cc_start: 0.7659 (t0) cc_final: 0.6921 (t0) REVERT: B 758 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8996 (tp) REVERT: B 930 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8240 (mmm) REVERT: C 84 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: C 269 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7068 (pt) REVERT: D 61 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7322 (mmp-170) REVERT: D 107 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.5987 (t80) REVERT: D 134 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7110 (p90) REVERT: D 237 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8418 (mppt) REVERT: D 269 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7184 (pp) REVERT: E 26 ASP cc_start: 0.8302 (t0) cc_final: 0.8067 (t0) REVERT: E 28 GLU cc_start: 0.7917 (mp0) cc_final: 0.7380 (mt-10) REVERT: E 37 LYS cc_start: 0.7511 (tptm) cc_final: 0.7039 (ttpt) outliers start: 97 outliers final: 35 residues processed: 345 average time/residue: 1.1290 time to fit residues: 454.7151 Evaluate side-chains 309 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 258 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER 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 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 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 108 SER 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 203 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 349 HIS B 765 ASN B 797 ASN B 948 ASN D 115 ASN D 118 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21923 Z= 0.207 Angle : 0.504 9.864 29610 Z= 0.262 Chirality : 0.040 0.340 3164 Planarity : 0.003 0.041 3744 Dihedral : 7.888 85.951 3040 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.75 % Allowed : 27.42 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2517 helix: 1.32 (0.13), residues: 1548 sheet: -0.60 (0.63), residues: 58 loop : -0.07 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.015 0.001 PHE B 699 TYR 0.015 0.001 TYR B 92 ARG 0.006 0.000 ARG B 747 *********************** 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 374 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 286 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7138 (mpp-170) REVERT: A 62 LEU cc_start: 0.8118 (mm) cc_final: 0.7843 (mm) REVERT: A 134 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: A 436 TYR cc_start: 0.8309 (t80) cc_final: 0.7996 (t80) REVERT: A 517 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.7952 (mtm110) REVERT: A 567 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 674 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7909 (t70) REVERT: A 784 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7185 (mp0) REVERT: A 787 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6220 (tt) REVERT: A 844 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 961 ASN cc_start: 0.8336 (m110) cc_final: 0.8109 (m110) REVERT: A 974 LYS cc_start: 0.7813 (pptt) cc_final: 0.7214 (pmmt) REVERT: B 17 GLU cc_start: 0.6912 (pt0) cc_final: 0.6652 (tp30) REVERT: B 54 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 69 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: B 188 ASP cc_start: 0.8542 (m-30) cc_final: 0.8246 (m-30) REVERT: B 502 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6083 (pmt-80) REVERT: B 504 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.4973 (t80) REVERT: B 521 ASN cc_start: 0.7650 (t0) cc_final: 0.6929 (t0) REVERT: B 758 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 866 MET cc_start: 0.7447 (mmm) cc_final: 0.7190 (mmp) REVERT: B 884 LEU cc_start: 0.7901 (tp) cc_final: 0.7323 (tp) REVERT: B 887 GLU cc_start: 0.7851 (pp20) cc_final: 0.7426 (pp20) REVERT: B 930 MET cc_start: 0.8437 (mtp) cc_final: 0.8156 (mmm) REVERT: B 981 ILE cc_start: 0.7826 (mm) cc_final: 0.7603 (mm) REVERT: C 84 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: C 119 ASP cc_start: 0.7524 (m-30) cc_final: 0.6810 (p0) REVERT: C 237 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7664 (tmmt) REVERT: C 269 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7127 (pt) REVERT: D 107 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.5914 (t80) REVERT: D 134 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7069 (p90) REVERT: D 212 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7532 (p) REVERT: D 227 MET cc_start: 0.7995 (mmp) cc_final: 0.7654 (pp-130) REVERT: D 237 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8415 (mppt) REVERT: D 269 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (pp) REVERT: D 274 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7836 (tp) REVERT: E 26 ASP cc_start: 0.8248 (t0) cc_final: 0.7987 (t0) REVERT: E 28 GLU cc_start: 0.7944 (mp0) cc_final: 0.7459 (mt-10) REVERT: E 37 LYS cc_start: 0.7514 (tptm) cc_final: 0.7034 (ttpt) outliers start: 88 outliers final: 37 residues processed: 347 average time/residue: 1.0772 time to fit residues: 436.9014 Evaluate side-chains 317 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 54 SER 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 294 ILE Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER 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 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LYS 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 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 82 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21923 Z= 0.299 Angle : 0.548 9.646 29610 Z= 0.285 Chirality : 0.042 0.354 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.866 86.054 3038 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.39 % Allowed : 27.63 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2517 helix: 1.15 (0.13), residues: 1554 sheet: -0.64 (0.63), residues: 58 loop : -0.28 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.017 0.002 PHE B 699 TYR 0.023 0.002 TYR A 324 ARG 0.006 0.000 ARG D 61 *********************** 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 378 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 275 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8097 (mm) cc_final: 0.7798 (mm) REVERT: A 134 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: A 295 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7294 (mt-10) REVERT: A 370 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6770 (mmt90) REVERT: A 517 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.7932 (mtm110) REVERT: A 567 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 674 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7861 (t70) REVERT: A 784 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7173 (mp0) REVERT: A 787 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.6176 (tt) REVERT: A 844 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 913 MET cc_start: 0.7431 (mtm) cc_final: 0.7203 (mtp) REVERT: A 961 ASN cc_start: 0.8346 (m110) cc_final: 0.8097 (m110) REVERT: A 974 LYS cc_start: 0.7893 (pptt) cc_final: 0.7240 (pmmt) REVERT: B 17 GLU cc_start: 0.6921 (pt0) cc_final: 0.6675 (tp30) REVERT: B 188 ASP cc_start: 0.8539 (m-30) cc_final: 0.8224 (m-30) REVERT: B 279 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: B 502 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6072 (pmt-80) REVERT: B 504 TYR cc_start: 0.5839 (OUTLIER) cc_final: 0.5033 (t80) REVERT: B 521 ASN cc_start: 0.7677 (t0) cc_final: 0.6936 (t0) REVERT: B 758 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9048 (tp) REVERT: B 930 MET cc_start: 0.8350 (mtp) cc_final: 0.8132 (mmm) REVERT: B 981 ILE cc_start: 0.7799 (mm) cc_final: 0.7516 (mm) REVERT: C 119 ASP cc_start: 0.7522 (m-30) cc_final: 0.6814 (p0) REVERT: C 134 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.6899 (p90) REVERT: C 165 ARG cc_start: 0.7568 (ptm160) cc_final: 0.7237 (ptm160) REVERT: C 237 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7713 (tmmt) REVERT: C 269 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7198 (pt) REVERT: D 107 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.5912 (t80) REVERT: D 134 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7411 (p90) REVERT: D 212 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7528 (p) REVERT: D 227 MET cc_start: 0.8045 (mmp) cc_final: 0.7656 (pp-130) REVERT: D 237 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8421 (mppt) REVERT: E 26 ASP cc_start: 0.8274 (t0) cc_final: 0.7996 (t0) REVERT: E 34 SER cc_start: 0.7935 (p) cc_final: 0.7651 (m) REVERT: E 37 LYS cc_start: 0.7505 (tptm) cc_final: 0.7055 (ttpt) outliers start: 103 outliers final: 39 residues processed: 345 average time/residue: 1.1047 time to fit residues: 446.7717 Evaluate side-chains 319 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 SER 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 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 915 THR 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 299 ASN Chi-restraints excluded: chain B residue 419 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER 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 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP 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 E residue 11 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 0.0570 chunk 27 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 243 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 115 ASN B 236 GLN B 349 HIS B 797 ASN B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1871 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= 0.168 Angle : 0.506 10.819 29610 Z= 0.263 Chirality : 0.039 0.345 3164 Planarity : 0.003 0.041 3744 Dihedral : 7.501 86.057 3038 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.24 % Allowed : 28.36 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2517 helix: 1.33 (0.13), residues: 1542 sheet: -0.65 (0.65), residues: 58 loop : -0.13 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.014 0.001 PHE B 699 TYR 0.017 0.001 TYR B 92 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7708 (mmt90) cc_final: 0.7124 (mpp-170) REVERT: A 62 LEU cc_start: 0.8074 (mm) cc_final: 0.7778 (mm) REVERT: A 134 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: A 236 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7168 (mm110) REVERT: A 274 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 436 TYR cc_start: 0.7891 (t80) cc_final: 0.7612 (t80) REVERT: A 517 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.7938 (mtm110) REVERT: A 567 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 674 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7900 (t70) REVERT: A 693 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7524 (pt0) REVERT: A 784 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7252 (mp0) REVERT: A 787 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6228 (tt) REVERT: A 844 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7493 (mp) REVERT: A 936 MET cc_start: 0.5180 (mpp) cc_final: 0.4235 (mmt) REVERT: A 961 ASN cc_start: 0.8360 (m110) cc_final: 0.8117 (m110) REVERT: A 974 LYS cc_start: 0.7710 (pptt) cc_final: 0.7154 (pmmt) REVERT: B 17 GLU cc_start: 0.6847 (pt0) cc_final: 0.6587 (tp30) REVERT: B 69 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 107 PHE cc_start: 0.7462 (m-80) cc_final: 0.7200 (m-10) REVERT: B 188 ASP cc_start: 0.8535 (m-30) cc_final: 0.8234 (m-30) REVERT: B 502 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6109 (pmt-80) REVERT: B 504 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.4957 (t80) REVERT: B 521 ASN cc_start: 0.7645 (t0) cc_final: 0.6891 (t0) REVERT: B 636 PHE cc_start: 0.5001 (m-80) cc_final: 0.4653 (m-80) REVERT: B 758 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8972 (tp) REVERT: B 866 MET cc_start: 0.7438 (mmm) cc_final: 0.7198 (mmp) REVERT: B 936 MET cc_start: 0.2912 (pmm) cc_final: 0.2379 (pmm) REVERT: B 981 ILE cc_start: 0.7778 (mm) cc_final: 0.7577 (mm) REVERT: B 1005 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7413 (tt) REVERT: C 56 TYR cc_start: 0.7816 (t80) cc_final: 0.7593 (t80) REVERT: C 84 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: C 119 ASP cc_start: 0.7208 (m-30) cc_final: 0.6616 (p0) REVERT: C 134 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6805 (p90) REVERT: C 165 ARG cc_start: 0.7520 (ptm160) cc_final: 0.7180 (ptm160) REVERT: C 269 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7197 (pt) REVERT: D 107 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.5876 (t80) REVERT: D 134 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7210 (p90) REVERT: D 212 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7479 (p) REVERT: D 227 MET cc_start: 0.8015 (mmp) cc_final: 0.7684 (pp-130) REVERT: D 237 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8403 (mppt) REVERT: D 274 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7783 (tt) REVERT: E 26 ASP cc_start: 0.8241 (t0) cc_final: 0.7957 (t0) REVERT: E 28 GLU cc_start: 0.7891 (mp0) cc_final: 0.7380 (mt-10) REVERT: E 37 LYS cc_start: 0.7509 (tptm) cc_final: 0.7041 (ttpt) outliers start: 76 outliers final: 34 residues processed: 345 average time/residue: 1.1808 time to fit residues: 473.7519 Evaluate side-chains 317 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 SER 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 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 294 ILE Chi-restraints excluded: chain B residue 299 ASN 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain B residue 1005 ILE 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS A 927 ASN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21923 Z= 0.169 Angle : 0.512 10.947 29610 Z= 0.265 Chirality : 0.039 0.357 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.358 86.629 3037 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.20 % Allowed : 28.78 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2517 helix: 1.36 (0.13), residues: 1544 sheet: -0.76 (0.61), residues: 64 loop : -0.13 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.017 0.001 PHE B 916 TYR 0.019 0.001 TYR A 324 ARG 0.007 0.000 ARG B 747 *********************** 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 365 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 290 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7710 (mmt90) cc_final: 0.7149 (mpp-170) REVERT: A 62 LEU cc_start: 0.8086 (mm) cc_final: 0.7823 (mm) REVERT: A 134 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: A 236 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7183 (mm110) REVERT: A 274 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7969 (tp) REVERT: A 436 TYR cc_start: 0.8074 (t80) cc_final: 0.7736 (t80) REVERT: A 517 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.7941 (mtm110) REVERT: A 567 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 674 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7910 (t70) REVERT: A 693 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7508 (pt0) REVERT: A 784 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7249 (mp0) REVERT: A 787 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6235 (tt) REVERT: A 844 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 856 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.4847 (t80) REVERT: A 936 MET cc_start: 0.5146 (mpp) cc_final: 0.4255 (mmt) REVERT: A 961 ASN cc_start: 0.8390 (m110) cc_final: 0.8170 (m110) REVERT: A 974 LYS cc_start: 0.7610 (pptt) cc_final: 0.7065 (pmmt) REVERT: B 17 GLU cc_start: 0.6913 (pt0) cc_final: 0.6643 (tp30) REVERT: B 107 PHE cc_start: 0.7595 (m-80) cc_final: 0.7114 (m-80) REVERT: B 188 ASP cc_start: 0.8516 (m-30) cc_final: 0.8212 (m-30) REVERT: B 502 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6092 (pmt-80) REVERT: B 504 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4939 (t80) REVERT: B 521 ASN cc_start: 0.7680 (t0) cc_final: 0.6914 (t0) REVERT: B 636 PHE cc_start: 0.4988 (m-80) cc_final: 0.4530 (m-80) REVERT: B 758 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8970 (tp) REVERT: B 926 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7621 (p0) REVERT: B 981 ILE cc_start: 0.7751 (mm) cc_final: 0.7539 (mm) REVERT: B 1005 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7385 (tt) REVERT: C 84 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: C 119 ASP cc_start: 0.7226 (m-30) cc_final: 0.6603 (p0) REVERT: C 134 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6839 (p90) REVERT: C 165 ARG cc_start: 0.7454 (ptm160) cc_final: 0.7104 (ptm160) REVERT: C 237 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7705 (tmmt) REVERT: C 269 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7234 (pt) REVERT: D 107 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5897 (t80) REVERT: D 124 MET cc_start: 0.7554 (mmm) cc_final: 0.7241 (mmm) REVERT: D 134 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7182 (p90) REVERT: D 212 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7393 (p) REVERT: D 227 MET cc_start: 0.8011 (mmp) cc_final: 0.7674 (pp-130) REVERT: D 237 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8394 (mppt) REVERT: D 274 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7801 (tt) REVERT: E 26 ASP cc_start: 0.8262 (t0) cc_final: 0.7979 (t0) REVERT: E 28 GLU cc_start: 0.7798 (mp0) cc_final: 0.7440 (mt-10) REVERT: E 37 LYS cc_start: 0.7491 (tptm) cc_final: 0.7027 (ttpt) REVERT: E 41 LYS cc_start: 0.7461 (mttm) cc_final: 0.6955 (mmpt) outliers start: 75 outliers final: 33 residues processed: 341 average time/residue: 1.1025 time to fit residues: 444.4601 Evaluate side-chains 326 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 SER 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 848 ASN Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 911 ASP 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 299 ASN 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1005 ILE 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 237 LYS 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 226 optimal weight: 0.0570 chunk 149 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2116 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= 0.167 Angle : 0.514 11.012 29610 Z= 0.267 Chirality : 0.039 0.356 3164 Planarity : 0.003 0.041 3744 Dihedral : 7.223 86.777 3037 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.99 % Allowed : 29.13 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2517 helix: 1.39 (0.13), residues: 1551 sheet: -0.73 (0.61), residues: 64 loop : -0.15 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 958 HIS 0.012 0.001 HIS B 349 PHE 0.020 0.001 PHE B 916 TYR 0.018 0.001 TYR A 940 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 293 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7707 (mmt90) cc_final: 0.7139 (mpp-170) REVERT: A 62 LEU cc_start: 0.8039 (mm) cc_final: 0.7761 (mm) REVERT: A 134 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.5861 (m-80) REVERT: A 236 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7174 (mm110) REVERT: A 274 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 436 TYR cc_start: 0.8070 (t80) cc_final: 0.7731 (t80) REVERT: A 517 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.7935 (mtm110) REVERT: A 525 ASP cc_start: 0.8354 (m-30) cc_final: 0.8085 (m-30) REVERT: A 567 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 674 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7908 (t70) REVERT: A 693 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7515 (pt0) REVERT: A 784 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7177 (mp0) REVERT: A 787 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6102 (tt) REVERT: A 844 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 913 MET cc_start: 0.7606 (mtp) cc_final: 0.7370 (ttt) REVERT: A 936 MET cc_start: 0.5055 (mpp) cc_final: 0.4152 (mmt) REVERT: A 961 ASN cc_start: 0.8353 (m110) cc_final: 0.8140 (m110) REVERT: A 974 LYS cc_start: 0.7573 (pptt) cc_final: 0.7040 (pmmt) REVERT: B 17 GLU cc_start: 0.6904 (pt0) cc_final: 0.6622 (tp30) REVERT: B 65 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (ttpp) REVERT: B 107 PHE cc_start: 0.6876 (m-80) cc_final: 0.6445 (m-80) REVERT: B 188 ASP cc_start: 0.8503 (m-30) cc_final: 0.8201 (m-30) REVERT: B 279 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 502 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6101 (pmt-80) REVERT: B 504 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.4943 (t80) REVERT: B 521 ASN cc_start: 0.7722 (t0) cc_final: 0.6970 (t0) REVERT: B 636 PHE cc_start: 0.4972 (m-80) cc_final: 0.4425 (m-80) REVERT: B 866 MET cc_start: 0.7258 (mmm) cc_final: 0.7016 (mmp) REVERT: B 926 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7577 (p0) REVERT: B 936 MET cc_start: 0.2913 (pmm) cc_final: 0.2424 (pmm) REVERT: C 84 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: C 134 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6746 (p90) REVERT: C 165 ARG cc_start: 0.7463 (ptm160) cc_final: 0.7118 (ptm160) REVERT: C 237 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7702 (tmmt) REVERT: C 269 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7286 (pt) REVERT: D 82 ASP cc_start: 0.7298 (m-30) cc_final: 0.6926 (p0) REVERT: D 107 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.5927 (t80) REVERT: D 124 MET cc_start: 0.7551 (mmm) cc_final: 0.7260 (mmm) REVERT: D 134 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7176 (p90) REVERT: D 227 MET cc_start: 0.8049 (mmp) cc_final: 0.7675 (pp-130) REVERT: D 237 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8389 (mppt) REVERT: E 20 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7833 (pt) REVERT: E 26 ASP cc_start: 0.8295 (t0) cc_final: 0.7982 (t0) REVERT: E 28 GLU cc_start: 0.7805 (mp0) cc_final: 0.7369 (mt-10) REVERT: E 37 LYS cc_start: 0.7496 (tptm) cc_final: 0.6998 (ttpt) REVERT: E 41 LYS cc_start: 0.7485 (mttm) cc_final: 0.6982 (mmpt) outliers start: 70 outliers final: 31 residues processed: 341 average time/residue: 1.1142 time to fit residues: 444.2054 Evaluate side-chains 321 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 271 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 65 LYS 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 299 ASN 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LYS 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 252 optimal weight: 0.0970 chunk 231 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 948 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2175 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= 0.186 Angle : 0.528 11.054 29610 Z= 0.273 Chirality : 0.040 0.360 3164 Planarity : 0.003 0.041 3744 Dihedral : 7.172 86.852 3037 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.43 % Allowed : 29.94 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2517 helix: 1.38 (0.13), residues: 1551 sheet: -0.70 (0.61), residues: 64 loop : -0.16 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.053 0.001 PHE B 942 TYR 0.019 0.001 TYR B 92 ARG 0.008 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 280 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7720 (mmt90) cc_final: 0.7132 (mpp-170) REVERT: A 62 LEU cc_start: 0.8036 (mm) cc_final: 0.7724 (mm) REVERT: A 134 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: A 236 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7176 (mm110) REVERT: A 274 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7976 (tp) REVERT: A 339 HIS cc_start: 0.7869 (m90) cc_final: 0.7552 (m90) REVERT: A 436 TYR cc_start: 0.8148 (t80) cc_final: 0.7832 (t80) REVERT: A 517 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.7925 (mtm110) REVERT: A 525 ASP cc_start: 0.8342 (m-30) cc_final: 0.8080 (m-30) REVERT: A 567 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 674 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7900 (t70) REVERT: A 693 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7518 (pt0) REVERT: A 784 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7214 (mp0) REVERT: A 787 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6110 (tt) REVERT: A 844 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (mp) REVERT: A 936 MET cc_start: 0.5019 (mpp) cc_final: 0.4158 (mmt) REVERT: A 961 ASN cc_start: 0.8356 (m110) cc_final: 0.8141 (m110) REVERT: A 974 LYS cc_start: 0.7588 (pptt) cc_final: 0.7034 (pmmt) REVERT: B 17 GLU cc_start: 0.6873 (pt0) cc_final: 0.6599 (tp30) REVERT: B 107 PHE cc_start: 0.6734 (m-80) cc_final: 0.6380 (m-80) REVERT: B 119 ASP cc_start: 0.8144 (m-30) cc_final: 0.7939 (m-30) REVERT: B 188 ASP cc_start: 0.8485 (m-30) cc_final: 0.8179 (m-30) REVERT: B 306 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6727 (t0) REVERT: B 502 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6014 (pmt-80) REVERT: B 521 ASN cc_start: 0.7688 (t0) cc_final: 0.6914 (t0) REVERT: B 636 PHE cc_start: 0.4967 (m-80) cc_final: 0.4402 (m-80) REVERT: B 936 MET cc_start: 0.3079 (pmm) cc_final: 0.2586 (pmm) REVERT: C 84 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7214 (m-10) REVERT: C 119 ASP cc_start: 0.7200 (m-30) cc_final: 0.6570 (p0) REVERT: C 134 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6609 (p90) REVERT: C 165 ARG cc_start: 0.7427 (ptm160) cc_final: 0.7029 (ptm160) REVERT: C 237 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7716 (tmmt) REVERT: C 269 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7302 (pt) REVERT: D 82 ASP cc_start: 0.7299 (m-30) cc_final: 0.6935 (p0) REVERT: D 107 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5900 (t80) REVERT: D 124 MET cc_start: 0.7690 (mmm) cc_final: 0.7468 (mmm) REVERT: D 134 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7180 (p90) REVERT: D 227 MET cc_start: 0.8054 (mmp) cc_final: 0.7675 (pp-130) REVERT: D 237 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8396 (mppt) REVERT: E 20 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7779 (pt) REVERT: E 26 ASP cc_start: 0.8272 (t0) cc_final: 0.7959 (t0) REVERT: E 28 GLU cc_start: 0.7824 (mp0) cc_final: 0.7433 (mt-10) REVERT: E 34 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7733 (m) REVERT: E 37 LYS cc_start: 0.7491 (tptm) cc_final: 0.6994 (ttpt) REVERT: E 41 LYS cc_start: 0.7474 (mttm) cc_final: 0.6944 (mmpt) outliers start: 57 outliers final: 33 residues processed: 317 average time/residue: 1.1298 time to fit residues: 416.4302 Evaluate side-chains 330 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 854 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 299 ASN 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 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LYS 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 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 206 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 176 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 797 ASN B 948 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115674 restraints weight = 31966.441| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.19 r_work: 0.3322 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2169 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= 0.201 Angle : 0.528 11.070 29610 Z= 0.274 Chirality : 0.040 0.360 3164 Planarity : 0.003 0.042 3744 Dihedral : 7.148 86.647 3037 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.47 % Allowed : 30.11 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2517 helix: 1.37 (0.13), residues: 1549 sheet: -0.70 (0.61), residues: 64 loop : -0.16 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 919 HIS 0.012 0.001 HIS B 349 PHE 0.024 0.001 PHE B 942 TYR 0.020 0.001 TYR B 92 ARG 0.008 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8102.88 seconds wall clock time: 145 minutes 23.06 seconds (8723.06 seconds total)