Starting phenix.real_space_refine on Sun Aug 24 17:02:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.map" model { file = "/net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkn_37603/08_2025/8wkn_37603.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 13901 2.51 5 N 3492 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21526 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 8075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 8075 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 951} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 8113 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2238 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 265} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2242 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 5.41, per 1000 atoms: 0.25 Number of scatterers: 21526 At special positions: 0 Unit cell: (126.65, 106.25, 187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 4054 8.00 N 3492 7.00 C 13901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 936.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4966 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 12 sheets defined 65.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.903A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.700A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.845A 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 97 through 109 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.645A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.424A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.831A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' 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 233 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.909A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.691A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.569A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.587A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.699A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.756A pdb=" N ASP B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 496 removed outlier: 3.682A pdb=" N GLY B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.507A pdb=" N LEU B 527 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.589A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 551 through 572 removed outlier: 3.902A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 removed outlier: 4.124A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.720A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.606A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 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 699 removed outlier: 3.507A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.919A pdb=" N THR B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.846A 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 763 removed outlier: 3.544A pdb=" N LYS B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.192A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.695A pdb=" N GLU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.548A pdb=" N ILE B 835 " --> pdb=" O LYS B 831 " (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 862 through 872 Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 928 through 933 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 962 removed outlier: 3.781A pdb=" N TRP B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.515A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.661A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.810A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.766A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.791A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 158 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 233 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 282 through 298 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: 3.851A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.606A pdb=" N LYS A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.662A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.632A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.669A pdb=" N ASP A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.612A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.422A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.821A pdb=" N ASN A 563 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.506A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.800A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 604 " --> pdb=" O TRP A 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 604' Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.966A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.712A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.876A 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 786 Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.720A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.534A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.964A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 896 Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.743A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 977 through 991 Processing helix chain 'A' and resid 993 through 1004 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.762A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.784A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 4.000A 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 97 through 109 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.848A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.580A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.939A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.346A pdb=" N LYS C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) 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 223 through 235 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 281 through 297 removed outlier: 4.004A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 39 Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.837A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.799A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.573A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.794A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.732A pdb=" N ASP D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA D 159 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 161 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 removed outlier: 4.101A pdb=" N LYS D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) 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 234 removed outlier: 3.798A pdb=" N ASN D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 281 through 297 removed outlier: 3.750A pdb=" N GLN D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 106 removed outlier: 3.547A pdb=" N ILE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.146A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.319A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.943A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.465A pdb=" N VAL C 129 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 247 Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 169 removed outlier: 7.150A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AB1, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 72 removed outlier: 4.266A pdb=" N GLU E 115 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 87 through 88 1090 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.49: 12784 1.49 - 1.76: 9102 1.76 - 2.02: 131 2.02 - 2.29: 0 2.29 - 2.56: 3 Bond restraints: 22020 Sorted by residual: bond pdb=" C GLY D 177 " pdb=" N LYS D 179 " ideal model delta sigma weight residual 1.332 2.558 -1.226 1.40e-02 5.10e+03 7.67e+03 bond pdb=" C ILE B 934 " pdb=" N MET B 936 " ideal model delta sigma weight residual 1.332 2.540 -1.208 1.40e-02 5.10e+03 7.44e+03 bond pdb=" C GLY C 177 " pdb=" N LYS C 179 " ideal model delta sigma weight residual 1.332 2.492 -1.160 1.40e-02 5.10e+03 6.87e+03 bond pdb=" N GLY A 494 " pdb=" CA GLY A 494 " ideal model delta sigma weight residual 1.444 1.475 -0.031 9.30e-03 1.16e+04 1.12e+01 bond pdb=" N ILE B 934 " pdb=" CA ILE B 934 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.83e+00 ... (remaining 22015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.39: 29700 8.39 - 16.77: 3 16.77 - 25.16: 1 25.16 - 33.54: 2 33.54 - 41.93: 2 Bond angle restraints: 29708 Sorted by residual: angle pdb=" O GLY C 177 " pdb=" C GLY C 177 " pdb=" N LYS C 179 " ideal model delta sigma weight residual 122.70 80.77 41.93 1.30e+00 5.92e-01 1.04e+03 angle pdb=" O GLY D 177 " pdb=" C GLY D 177 " pdb=" N LYS D 179 " ideal model delta sigma weight residual 122.70 86.55 36.15 1.30e+00 5.92e-01 7.73e+02 angle pdb=" O ILE B 934 " pdb=" C ILE B 934 " pdb=" N MET B 936 " ideal model delta sigma weight residual 123.20 94.33 28.87 1.06e+00 8.90e-01 7.42e+02 angle pdb=" C ILE B 934 " pdb=" N MET B 936 " pdb=" CA MET B 936 " ideal model delta sigma weight residual 121.54 147.61 -26.07 1.91e+00 2.74e-01 1.86e+02 angle pdb=" C GLY D 177 " pdb=" N LYS D 179 " pdb=" CA LYS D 179 " ideal model delta sigma weight residual 121.54 141.99 -20.45 1.91e+00 2.74e-01 1.15e+02 ... (remaining 29703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11275 17.75 - 35.50: 1465 35.50 - 53.26: 319 53.26 - 71.01: 51 71.01 - 88.76: 11 Dihedral angle restraints: 13121 sinusoidal: 5395 harmonic: 7726 Sorted by residual: dihedral pdb=" CA ILE B 934 " pdb=" C ILE B 934 " pdb=" N MET B 936 " pdb=" CA MET B 936 " ideal model delta harmonic sigma weight residual 180.00 -93.53 -86.47 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA GLY C 177 " pdb=" C GLY C 177 " pdb=" N LYS C 179 " pdb=" CA LYS C 179 " ideal model delta harmonic sigma weight residual 180.00 145.49 34.51 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ALA E 60 " pdb=" C ALA E 60 " pdb=" N VAL E 61 " pdb=" CA VAL E 61 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 13118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2297 0.040 - 0.079: 698 0.079 - 0.119: 165 0.119 - 0.158: 16 0.158 - 0.198: 4 Chirality restraints: 3180 Sorted by residual: chirality pdb=" CA ASN C 125 " pdb=" N ASN C 125 " pdb=" C ASN C 125 " pdb=" CB ASN C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA ILE B 934 " pdb=" N ILE B 934 " pdb=" C ILE B 934 " pdb=" CB ILE B 934 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA LYS C 176 " pdb=" N LYS C 176 " pdb=" C LYS C 176 " pdb=" CB LYS C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 3177 not shown) Planarity restraints: 3797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 177 " 0.192 2.00e-02 2.50e+03 2.75e-01 7.56e+02 pdb=" C GLY C 177 " -0.461 2.00e-02 2.50e+03 pdb=" O GLY C 177 " 0.226 2.00e-02 2.50e+03 pdb=" N LYS C 179 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 177 " 0.174 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C GLY D 177 " -0.413 2.00e-02 2.50e+03 pdb=" O GLY D 177 " 0.179 2.00e-02 2.50e+03 pdb=" N LYS D 179 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 934 " 0.150 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C ILE B 934 " -0.370 2.00e-02 2.50e+03 pdb=" O ILE B 934 " 0.158 2.00e-02 2.50e+03 pdb=" N MET B 936 " 0.063 2.00e-02 2.50e+03 ... (remaining 3794 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2872 2.75 - 3.29: 20802 3.29 - 3.83: 34833 3.83 - 4.36: 38974 4.36 - 4.90: 69144 Nonbonded interactions: 166625 Sorted by model distance: nonbonded pdb=" OH TYR B 71 " pdb=" OG1 THR C 257 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 80 " pdb=" OD1 ASP A 82 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 927 " pdb=" N LYS A 929 " model vdw 2.222 3.120 nonbonded pdb=" OE1 GLU B 341 " pdb=" OG1 THR B 345 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR E 16 " pdb=" OD1 ASN E 21 " model vdw 2.227 3.040 ... (remaining 166620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 504 or (resid 505 and \ (name N or name CA or name C or name O or name CB )) or resid 506 through 637 or \ (resid 638 through 639 and (name N or name CA or name C or name O or name CB )) \ or resid 640 through 747 or resid 749 through 896 or resid 910 through 934 or r \ esid 936 through 1005)) selection = (chain 'B' and (resid 22 through 566 or resid 578 through 787 or resid 789 throu \ gh 896 or resid 910 through 911 or (resid 912 and (name N or name CA or name C o \ r name O or name CB )) or resid 913 through 974 or resid 976 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 23 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB )) or resid 106 through 299)) } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.210 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 : 0.014 1.226 22020 Z= 1.011 Angle : 0.673 41.925 29708 Z= 0.424 Chirality : 0.040 0.198 3180 Planarity : 0.008 0.275 3797 Dihedral : 16.083 88.762 8155 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 0.30 % Allowed : 19.00 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2577 helix: 1.68 (0.14), residues: 1451 sheet: -1.18 (0.40), residues: 157 loop : -1.20 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 285 TYR 0.017 0.001 TYR C 280 PHE 0.035 0.001 PHE B 636 TRP 0.021 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.01432 (22020) covalent geometry : angle 0.67298 (29708) hydrogen bonds : bond 0.15062 ( 1090) hydrogen bonds : angle 5.22546 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 504 TYR cc_start: 0.7123 (m-80) cc_final: 0.6521 (m-80) REVERT: A 860 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7040 (mp0) outliers start: 7 outliers final: 4 residues processed: 191 average time/residue: 0.1491 time to fit residues: 44.6879 Evaluate side-chains 180 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 41 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 483 GLN B 487 GLN A 487 GLN A 503 HIS A 867 ASN A 939 GLN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 171 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069980 restraints weight = 47550.265| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.91 r_work: 0.2824 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22020 Z= 0.140 Angle : 0.508 10.618 29708 Z= 0.268 Chirality : 0.039 0.161 3180 Planarity : 0.004 0.053 3797 Dihedral : 4.168 55.222 2870 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 17.95 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.17), residues: 2583 helix: 1.83 (0.14), residues: 1482 sheet: -1.60 (0.39), residues: 147 loop : -1.16 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.013 0.001 TYR D 286 PHE 0.019 0.001 PHE B 636 TRP 0.013 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00327 (22020) covalent geometry : angle 0.50797 (29708) hydrogen bonds : bond 0.04382 ( 1090) hydrogen bonds : angle 4.08329 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 860 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 1001 MET cc_start: 0.9160 (mmm) cc_final: 0.8714 (mmm) REVERT: A 134 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8061 (p90) REVERT: A 892 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8706 (mtp-110) REVERT: C 190 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 223 TYR cc_start: 0.7005 (t80) cc_final: 0.6792 (t80) outliers start: 36 outliers final: 14 residues processed: 219 average time/residue: 0.1408 time to fit residues: 47.4636 Evaluate side-chains 194 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 210 optimal weight: 4.9990 chunk 255 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN D 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069212 restraints weight = 47630.016| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.93 r_work: 0.2797 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22020 Z= 0.155 Angle : 0.498 10.721 29708 Z= 0.261 Chirality : 0.039 0.153 3180 Planarity : 0.004 0.053 3797 Dihedral : 3.902 19.021 2859 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 1.82 % Allowed : 18.12 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2583 helix: 1.88 (0.14), residues: 1484 sheet: -1.61 (0.39), residues: 147 loop : -1.16 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 175 TYR 0.012 0.001 TYR D 286 PHE 0.019 0.001 PHE B 636 TRP 0.010 0.001 TRP D 143 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00368 (22020) covalent geometry : angle 0.49837 (29708) hydrogen bonds : bond 0.04233 ( 1090) hydrogen bonds : angle 3.93015 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8145 (mtp85) REVERT: B 1001 MET cc_start: 0.9175 (mmm) cc_final: 0.8737 (mmm) REVERT: A 134 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7989 (p90) REVERT: A 237 LYS cc_start: 0.8845 (tppt) cc_final: 0.8626 (tppt) REVERT: A 892 ARG cc_start: 0.9092 (ttm110) cc_final: 0.8766 (mtp-110) REVERT: A 998 GLU cc_start: 0.8883 (tt0) cc_final: 0.8615 (tt0) REVERT: C 247 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6529 (ttt180) outliers start: 43 outliers final: 23 residues processed: 214 average time/residue: 0.1291 time to fit residues: 43.1838 Evaluate side-chains 199 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 249 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.103893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072194 restraints weight = 48814.551| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.09 r_work: 0.2944 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22020 Z= 0.244 Angle : 0.565 11.716 29708 Z= 0.294 Chirality : 0.042 0.154 3180 Planarity : 0.004 0.053 3797 Dihedral : 4.115 19.310 2859 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 2.32 % Allowed : 17.86 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.17), residues: 2583 helix: 1.71 (0.14), residues: 1492 sheet: -1.55 (0.40), residues: 142 loop : -1.26 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 145 TYR 0.015 0.001 TYR A 436 PHE 0.021 0.002 PHE B 636 TRP 0.012 0.001 TRP B 757 HIS 0.005 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00584 (22020) covalent geometry : angle 0.56549 (29708) hydrogen bonds : bond 0.04917 ( 1090) hydrogen bonds : angle 4.07097 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8162 (mtp85) REVERT: B 326 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8876 (ptt180) REVERT: B 677 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8214 (mtp85) REVERT: B 1001 MET cc_start: 0.9202 (mmm) cc_final: 0.8712 (mmm) REVERT: A 291 ASP cc_start: 0.9063 (m-30) cc_final: 0.8778 (m-30) REVERT: A 892 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8725 (mtp-110) REVERT: A 998 GLU cc_start: 0.8857 (tt0) cc_final: 0.8581 (tt0) REVERT: C 75 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7036 (ttpp) REVERT: E 93 LYS cc_start: 0.6873 (mppt) cc_final: 0.6297 (mppt) outliers start: 55 outliers final: 32 residues processed: 219 average time/residue: 0.1719 time to fit residues: 58.0764 Evaluate side-chains 208 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 111 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 HIS ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 118 HIS D 171 HIS D 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.105920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074313 restraints weight = 48347.983| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.11 r_work: 0.2971 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22020 Z= 0.126 Angle : 0.483 12.471 29708 Z= 0.252 Chirality : 0.039 0.145 3180 Planarity : 0.003 0.052 3797 Dihedral : 3.965 18.348 2859 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 2.20 % Allowed : 18.67 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2583 helix: 1.86 (0.14), residues: 1494 sheet: -1.56 (0.40), residues: 142 loop : -1.21 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 657 TYR 0.016 0.001 TYR C 223 PHE 0.015 0.001 PHE B 636 TRP 0.012 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00299 (22020) covalent geometry : angle 0.48323 (29708) hydrogen bonds : bond 0.03853 ( 1090) hydrogen bonds : angle 3.83570 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8160 (mtp85) REVERT: B 326 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8766 (ptt180) REVERT: B 1001 MET cc_start: 0.9197 (mmm) cc_final: 0.8815 (mmm) REVERT: A 109 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: A 291 ASP cc_start: 0.9032 (m-30) cc_final: 0.8756 (m-30) REVERT: A 998 GLU cc_start: 0.8828 (tt0) cc_final: 0.8567 (tt0) outliers start: 52 outliers final: 36 residues processed: 226 average time/residue: 0.1638 time to fit residues: 57.8813 Evaluate side-chains 210 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 258 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074566 restraints weight = 48380.398| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.15 r_work: 0.3001 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22020 Z= 0.116 Angle : 0.473 13.333 29708 Z= 0.246 Chirality : 0.039 0.152 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.855 17.776 2859 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.28 % Allowed : 18.50 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2583 helix: 1.96 (0.14), residues: 1495 sheet: -1.47 (0.38), residues: 154 loop : -1.17 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 677 TYR 0.013 0.001 TYR C 223 PHE 0.020 0.001 PHE A 500 TRP 0.015 0.001 TRP D 143 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00272 (22020) covalent geometry : angle 0.47251 (29708) hydrogen bonds : bond 0.03610 ( 1090) hydrogen bonds : angle 3.73820 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8742 (ptt180) REVERT: B 1001 MET cc_start: 0.9184 (mmm) cc_final: 0.8792 (mmm) REVERT: A 109 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: A 492 PHE cc_start: 0.7689 (m-80) cc_final: 0.7459 (t80) REVERT: A 998 GLU cc_start: 0.8802 (tt0) cc_final: 0.8544 (tt0) outliers start: 54 outliers final: 38 residues processed: 231 average time/residue: 0.1622 time to fit residues: 59.3504 Evaluate side-chains 221 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 132 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.105803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074325 restraints weight = 48294.408| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.10 r_work: 0.2995 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22020 Z= 0.141 Angle : 0.497 13.652 29708 Z= 0.256 Chirality : 0.039 0.156 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.855 17.796 2859 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.15 % Allowed : 18.92 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2583 helix: 1.95 (0.14), residues: 1495 sheet: -1.48 (0.38), residues: 154 loop : -1.16 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 145 TYR 0.013 0.001 TYR C 223 PHE 0.032 0.001 PHE B 636 TRP 0.024 0.001 TRP D 143 HIS 0.004 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00337 (22020) covalent geometry : angle 0.49698 (29708) hydrogen bonds : bond 0.03797 ( 1090) hydrogen bonds : angle 3.76328 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: B 326 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8772 (ptt180) REVERT: B 337 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (t0) REVERT: B 1001 MET cc_start: 0.9187 (mmm) cc_final: 0.8783 (mmm) REVERT: A 14 LYS cc_start: 0.7113 (tptt) cc_final: 0.6813 (tptt) REVERT: A 492 PHE cc_start: 0.7698 (m-80) cc_final: 0.7479 (t80) REVERT: A 998 GLU cc_start: 0.8819 (tt0) cc_final: 0.8558 (tt0) REVERT: C 28 GLU cc_start: 0.9082 (mp0) cc_final: 0.8687 (mp0) REVERT: C 115 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.6926 (t0) REVERT: D 175 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8705 (mtp-110) REVERT: D 290 MET cc_start: 0.8154 (ppp) cc_final: 0.7830 (ppp) outliers start: 51 outliers final: 41 residues processed: 223 average time/residue: 0.1638 time to fit residues: 57.5957 Evaluate side-chains 222 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066453 restraints weight = 47698.207| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.94 r_work: 0.2737 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22020 Z= 0.216 Angle : 0.550 13.986 29708 Z= 0.284 Chirality : 0.041 0.160 3180 Planarity : 0.004 0.054 3797 Dihedral : 4.034 19.310 2859 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 2.41 % Allowed : 18.92 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.17), residues: 2583 helix: 1.78 (0.14), residues: 1504 sheet: -1.55 (0.38), residues: 154 loop : -1.25 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 145 TYR 0.015 0.001 TYR C 223 PHE 0.019 0.001 PHE A 500 TRP 0.028 0.001 TRP D 143 HIS 0.006 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00518 (22020) covalent geometry : angle 0.55024 (29708) hydrogen bonds : bond 0.04539 ( 1090) hydrogen bonds : angle 3.92846 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8219 (mtp85) REVERT: B 326 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8904 (ptt180) REVERT: B 503 HIS cc_start: 0.6261 (t-170) cc_final: 0.5815 (t70) REVERT: A 14 LYS cc_start: 0.7204 (tptt) cc_final: 0.6921 (tptt) REVERT: A 998 GLU cc_start: 0.8951 (tt0) cc_final: 0.8677 (tt0) REVERT: C 115 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7012 (t0) REVERT: C 247 ARG cc_start: 0.7068 (ttt180) cc_final: 0.6836 (ttt180) REVERT: D 175 ARG cc_start: 0.8989 (mtp-110) cc_final: 0.8755 (mtp-110) REVERT: D 290 MET cc_start: 0.8143 (ppp) cc_final: 0.7771 (ppp) REVERT: E 41 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8485 (pptt) outliers start: 57 outliers final: 42 residues processed: 221 average time/residue: 0.1641 time to fit residues: 56.8850 Evaluate side-chains 217 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 174 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 186 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.107088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075365 restraints weight = 48130.882| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.14 r_work: 0.3020 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22020 Z= 0.096 Angle : 0.480 14.175 29708 Z= 0.248 Chirality : 0.039 0.173 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.823 18.158 2859 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 1.73 % Allowed : 19.64 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2583 helix: 1.98 (0.14), residues: 1499 sheet: -1.48 (0.38), residues: 156 loop : -1.14 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 145 TYR 0.013 0.001 TYR C 223 PHE 0.037 0.001 PHE B 636 TRP 0.028 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00214 (22020) covalent geometry : angle 0.48017 (29708) hydrogen bonds : bond 0.03289 ( 1090) hydrogen bonds : angle 3.69175 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8754 (ptt180) REVERT: B 337 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7936 (t0) REVERT: A 14 LYS cc_start: 0.7093 (tptt) cc_final: 0.6782 (tptt) REVERT: A 998 GLU cc_start: 0.8789 (tt0) cc_final: 0.8530 (tt0) REVERT: D 290 MET cc_start: 0.8130 (ppp) cc_final: 0.7762 (ppp) outliers start: 41 outliers final: 34 residues processed: 223 average time/residue: 0.1621 time to fit residues: 56.8008 Evaluate side-chains 212 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 134 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 217 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075837 restraints weight = 48428.959| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.12 r_work: 0.3026 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22020 Z= 0.100 Angle : 0.492 14.660 29708 Z= 0.252 Chirality : 0.039 0.178 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.732 16.978 2859 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.69 % Allowed : 20.10 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2583 helix: 2.03 (0.14), residues: 1498 sheet: -1.44 (0.38), residues: 156 loop : -1.10 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 760 TYR 0.015 0.001 TYR A 504 PHE 0.022 0.001 PHE A 500 TRP 0.030 0.001 TRP D 143 HIS 0.010 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00229 (22020) covalent geometry : angle 0.49189 (29708) hydrogen bonds : bond 0.03257 ( 1090) hydrogen bonds : angle 3.65485 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8757 (ptt180) REVERT: B 337 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 14 LYS cc_start: 0.7111 (tptt) cc_final: 0.6804 (tptt) REVERT: A 998 GLU cc_start: 0.8772 (tt0) cc_final: 0.8544 (tt0) REVERT: C 115 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7111 (t0) REVERT: C 297 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: D 290 MET cc_start: 0.8107 (ppp) cc_final: 0.7710 (ppp) outliers start: 40 outliers final: 29 residues processed: 214 average time/residue: 0.1612 time to fit residues: 54.7320 Evaluate side-chains 210 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 117 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 243 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075579 restraints weight = 48347.881| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.15 r_work: 0.3026 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.207 22020 Z= 0.168 Angle : 0.668 59.199 29708 Z= 0.377 Chirality : 0.045 1.305 3180 Planarity : 0.004 0.080 3797 Dihedral : 3.743 19.801 2859 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 1.48 % Allowed : 20.10 % Favored : 78.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2583 helix: 2.03 (0.14), residues: 1498 sheet: -1.44 (0.38), residues: 156 loop : -1.12 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 760 TYR 0.015 0.001 TYR A 504 PHE 0.020 0.001 PHE A 500 TRP 0.028 0.001 TRP D 143 HIS 0.009 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00333 (22020) covalent geometry : angle 0.66839 (29708) hydrogen bonds : bond 0.03250 ( 1090) hydrogen bonds : angle 3.65669 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.91 seconds wall clock time: 80 minutes 51.26 seconds (4851.26 seconds total)