Starting phenix.real_space_refine on Wed Jun 18 17:59:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkn_37603/06_2025/8wkn_37603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkn_37603/06_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_37603/06_2025/8wkn_37603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkn_37603/06_2025/8wkn_37603.map" model { file = "/net/cci-nas-00/data/ceres_data/8wkn_37603/06_2025/8wkn_37603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkn_37603/06_2025/8wkn_37603.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'ARG: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: {'TYR:plan': 1, 'ARG: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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 12.80, per 1000 atoms: 0.59 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: 5.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.58 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: 8.28 Time building geometry restraints manager: 6.17 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: 2.950 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.680 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.050 ------------------------------------------------------------------------------- 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 : 6.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (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 TRP 0.021 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.035 0.001 PHE B 636 TYR 0.017 0.001 TYR C 280 ARG 0.006 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.15062 ( 1090) hydrogen bonds : angle 5.22546 ( 3120) covalent geometry : bond 0.01432 (22020) covalent geometry : angle 0.67298 (29708) *********************** 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 : 2.651 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: 0.3536 time to fit residues: 105.6474 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 : 2.626 ------------------------------------------------------------------------------- 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 218 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068299 restraints weight = 47673.583| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.90 r_work: 0.2789 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22020 Z= 0.207 Angle : 0.548 10.733 29708 Z= 0.288 Chirality : 0.041 0.162 3180 Planarity : 0.004 0.053 3797 Dihedral : 4.281 56.322 2870 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 1.77 % Allowed : 18.37 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2583 helix: 1.73 (0.14), residues: 1483 sheet: -1.64 (0.39), residues: 147 loop : -1.19 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 143 HIS 0.004 0.001 HIS B 241 PHE 0.020 0.001 PHE B 636 TYR 0.013 0.001 TYR B 356 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 1090) hydrogen bonds : angle 4.18687 ( 3120) covalent geometry : bond 0.00493 (22020) covalent geometry : angle 0.54836 (29708) *********************** 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: 42 poor density : 188 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8039 (p90) REVERT: A 892 ARG cc_start: 0.9067 (ttm110) cc_final: 0.8728 (mtp-110) REVERT: C 190 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 223 TYR cc_start: 0.7206 (t80) cc_final: 0.6420 (t80) REVERT: C 247 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6410 (ttt180) REVERT: D 290 MET cc_start: 0.7715 (ppp) cc_final: 0.7510 (ppp) outliers start: 42 outliers final: 19 residues processed: 221 average time/residue: 0.3449 time to fit residues: 117.9490 Evaluate side-chains 195 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 134 TYR 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 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 D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 275 ILE 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 94 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 202 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075108 restraints weight = 48237.184| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.11 r_work: 0.3006 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22020 Z= 0.125 Angle : 0.482 10.851 29708 Z= 0.253 Chirality : 0.039 0.147 3180 Planarity : 0.004 0.054 3797 Dihedral : 3.918 18.766 2859 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.65 % Allowed : 18.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2583 helix: 1.86 (0.14), residues: 1494 sheet: -1.63 (0.39), residues: 147 loop : -1.20 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.021 0.001 PHE B 636 TYR 0.012 0.001 TYR D 286 ARG 0.003 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1090) hydrogen bonds : angle 3.89814 ( 3120) covalent geometry : bond 0.00292 (22020) covalent geometry : angle 0.48195 (29708) *********************** 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 225 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8137 (mtp85) REVERT: B 326 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8803 (ptt180) REVERT: B 1001 MET cc_start: 0.9215 (mmm) cc_final: 0.8830 (mmm) REVERT: A 134 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7954 (p90) REVERT: A 892 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8762 (mtp-110) REVERT: A 998 GLU cc_start: 0.8808 (tt0) cc_final: 0.8601 (tt0) REVERT: C 247 ARG cc_start: 0.6929 (ttt180) cc_final: 0.6497 (ttt180) REVERT: D 290 MET cc_start: 0.7561 (ppp) cc_final: 0.7335 (ppp) outliers start: 39 outliers final: 19 residues processed: 213 average time/residue: 0.3456 time to fit residues: 114.6950 Evaluate side-chains 196 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 326 ARG Chi-restraints excluded: chain B residue 936 MET 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 367 CYS 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 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 168 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.0370 chunk 100 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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** B 658 HIS A 979 HIS C 109 GLN C 118 HIS C 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077632 restraints weight = 48658.247| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.12 r_work: 0.3060 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22020 Z= 0.088 Angle : 0.453 11.628 29708 Z= 0.236 Chirality : 0.038 0.155 3180 Planarity : 0.003 0.055 3797 Dihedral : 3.709 18.080 2859 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 1.69 % Allowed : 18.33 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2583 helix: 2.01 (0.14), residues: 1494 sheet: -1.99 (0.40), residues: 127 loop : -1.03 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 143 HIS 0.002 0.000 HIS A 978 PHE 0.017 0.001 PHE A 500 TYR 0.012 0.001 TYR D 286 ARG 0.003 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1090) hydrogen bonds : angle 3.69538 ( 3120) covalent geometry : bond 0.00190 (22020) covalent geometry : angle 0.45280 (29708) *********************** 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 243 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 2.842 Fit side-chains revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8731 (ptt180) REVERT: A 134 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7937 (p90) REVERT: A 892 ARG cc_start: 0.9060 (ttm110) cc_final: 0.8668 (mtp-110) REVERT: C 75 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7064 (ttpp) REVERT: C 109 GLN cc_start: 0.9304 (tp40) cc_final: 0.9100 (tp-100) REVERT: C 190 TYR cc_start: 0.7716 (t80) cc_final: 0.7190 (t80) REVERT: C 223 TYR cc_start: 0.7121 (t80) cc_final: 0.6633 (t80) REVERT: C 280 TYR cc_start: 0.8111 (m-80) cc_final: 0.7851 (m-10) REVERT: D 23 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6083 (t0) REVERT: D 175 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8574 (mtp-110) REVERT: D 290 MET cc_start: 0.7537 (ppp) cc_final: 0.7172 (ppp) REVERT: E 28 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7678 (mm-30) outliers start: 40 outliers final: 18 residues processed: 232 average time/residue: 0.3502 time to fit residues: 127.0592 Evaluate side-chains 203 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 347 VAL 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 75 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 23 ASP 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 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 123 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 164 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071159 restraints weight = 46903.856| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.02 r_work: 0.2828 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1488 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= 0.090 Angle : 0.456 12.324 29708 Z= 0.236 Chirality : 0.038 0.148 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.641 17.939 2859 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 18.50 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2583 helix: 2.04 (0.14), residues: 1494 sheet: -1.38 (0.38), residues: 156 loop : -1.09 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 143 HIS 0.003 0.000 HIS B 978 PHE 0.013 0.001 PHE A 837 TYR 0.009 0.001 TYR D 286 ARG 0.002 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1090) hydrogen bonds : angle 3.63989 ( 3120) covalent geometry : bond 0.00199 (22020) covalent geometry : angle 0.45586 (29708) *********************** 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 235 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8765 (ptt180) REVERT: B 337 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7876 (t0) REVERT: A 109 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: A 134 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7964 (p90) REVERT: C 75 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7032 (ttpp) REVERT: C 115 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7162 (t0) REVERT: C 280 TYR cc_start: 0.8086 (m-80) cc_final: 0.7782 (m-10) REVERT: D 175 ARG cc_start: 0.8991 (mtp-110) cc_final: 0.8672 (mtp-110) REVERT: E 28 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7677 (mm-30) outliers start: 41 outliers final: 23 residues processed: 225 average time/residue: 0.3448 time to fit residues: 123.5208 Evaluate side-chains 208 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 711 GLN Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 75 LYS 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 195 GLN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 57 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074234 restraints weight = 48367.584| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.13 r_work: 0.2992 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22020 Z= 0.169 Angle : 0.511 12.952 29708 Z= 0.262 Chirality : 0.040 0.144 3180 Planarity : 0.004 0.052 3797 Dihedral : 3.757 18.080 2859 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 1.94 % Allowed : 18.96 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2583 helix: 1.99 (0.14), residues: 1497 sheet: -1.49 (0.39), residues: 144 loop : -1.07 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 143 HIS 0.005 0.001 HIS A 979 PHE 0.028 0.001 PHE B 636 TYR 0.012 0.001 TYR B 482 ARG 0.003 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1090) hydrogen bonds : angle 3.74538 ( 3120) covalent geometry : bond 0.00406 (22020) covalent geometry : angle 0.51119 (29708) *********************** 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 230 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 2.789 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8243 (mtp85) REVERT: B 326 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8855 (ptt180) REVERT: A 109 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: C 115 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7177 (t0) REVERT: E 28 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7778 (mm-30) outliers start: 46 outliers final: 32 residues processed: 220 average time/residue: 0.3356 time to fit residues: 116.8730 Evaluate side-chains 213 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 2.812 ------------------------------------------------------------------------------- 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 175 ARG 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 B residue 764 CYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 839 PHE 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 203 LEU 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 167 LEU Chi-restraints excluded: chain D residue 184 VAL 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 39 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 222 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 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 = 0.3507 r_free = 0.3507 target = 0.098875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.066923 restraints weight = 47759.394| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.96 r_work: 0.2751 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22020 Z= 0.229 Angle : 0.552 13.523 29708 Z= 0.285 Chirality : 0.041 0.178 3180 Planarity : 0.004 0.063 3797 Dihedral : 3.990 19.609 2859 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 2.20 % Allowed : 18.83 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2583 helix: 1.80 (0.14), residues: 1499 sheet: -1.58 (0.40), residues: 144 loop : -1.16 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 143 HIS 0.006 0.001 HIS A 979 PHE 0.020 0.001 PHE A 500 TYR 0.026 0.001 TYR C 223 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 1090) hydrogen bonds : angle 3.91975 ( 3120) covalent geometry : bond 0.00545 (22020) covalent geometry : angle 0.55231 (29708) *********************** 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 232 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8173 (mtp85) REVERT: B 326 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8945 (ptt180) REVERT: A 14 LYS cc_start: 0.7286 (tptt) cc_final: 0.6998 (tptt) REVERT: A 109 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: C 28 GLU cc_start: 0.9064 (mp0) cc_final: 0.8701 (mp0) REVERT: C 115 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7421 (t0) REVERT: E 28 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7812 (mm-30) outliers start: 52 outliers final: 37 residues processed: 218 average time/residue: 0.3679 time to fit residues: 127.0720 Evaluate side-chains 214 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain B residue 284 GLU 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 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 ASP 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 347 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 520 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 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE 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 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 47 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 224 ASN 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 = 0.106467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074472 restraints weight = 48452.404| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.15 r_work: 0.2999 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1656 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= 0.126 Angle : 0.492 14.138 29708 Z= 0.254 Chirality : 0.039 0.163 3180 Planarity : 0.003 0.055 3797 Dihedral : 3.888 18.046 2859 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.69 % Allowed : 19.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2583 helix: 1.93 (0.14), residues: 1495 sheet: -1.50 (0.38), residues: 156 loop : -1.12 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 143 HIS 0.008 0.001 HIS A 503 PHE 0.035 0.001 PHE B 636 TYR 0.022 0.001 TYR C 223 ARG 0.005 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1090) hydrogen bonds : angle 3.74436 ( 3120) covalent geometry : bond 0.00298 (22020) covalent geometry : angle 0.49212 (29708) *********************** 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 222 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8211 (mtp85) REVERT: B 326 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8774 (ptt180) REVERT: B 337 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7910 (t0) REVERT: A 14 LYS cc_start: 0.7114 (tptt) cc_final: 0.6798 (tptt) REVERT: A 109 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: A 504 TYR cc_start: 0.7991 (m-80) cc_final: 0.7658 (m-80) REVERT: C 115 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7498 (t0) REVERT: E 28 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7804 (mm-30) REVERT: E 41 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8421 (pptt) outliers start: 40 outliers final: 30 residues processed: 215 average time/residue: 0.4749 time to fit residues: 164.8679 Evaluate side-chains 211 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 6.123 ------------------------------------------------------------------------------- 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 175 ARG 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 A residue 52 THR 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 347 VAL Chi-restraints excluded: chain A residue 405 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 167 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 222 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 216 optimal weight: 0.0470 chunk 204 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.106912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075499 restraints weight = 48100.902| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.11 r_work: 0.3018 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1694 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= 0.109 Angle : 0.493 14.579 29708 Z= 0.253 Chirality : 0.039 0.173 3180 Planarity : 0.003 0.056 3797 Dihedral : 3.819 17.577 2859 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 1.73 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2583 helix: 1.99 (0.14), residues: 1495 sheet: -1.44 (0.38), residues: 156 loop : -1.09 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 143 HIS 0.003 0.001 HIS A 979 PHE 0.021 0.001 PHE A 500 TYR 0.019 0.001 TYR C 223 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1090) hydrogen bonds : angle 3.69118 ( 3120) covalent geometry : bond 0.00253 (22020) covalent geometry : angle 0.49333 (29708) *********************** 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 218 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 2.224 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8222 (mtp85) REVERT: B 326 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8765 (ptt180) REVERT: B 337 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7894 (t0) REVERT: A 109 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: C 297 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: D 290 MET cc_start: 0.7952 (ppp) cc_final: 0.7659 (ppp) REVERT: E 28 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7798 (mm-30) REVERT: E 41 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (pptt) REVERT: E 93 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7130 (mmtm) outliers start: 41 outliers final: 30 residues processed: 209 average time/residue: 0.3875 time to fit residues: 127.0689 Evaluate side-chains 213 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 3.292 ------------------------------------------------------------------------------- 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 175 ARG 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 A residue 52 THR 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 347 VAL Chi-restraints excluded: chain A residue 405 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 134 TYR Chi-restraints excluded: chain C residue 167 LEU 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 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 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 93 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 149 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076150 restraints weight = 48426.738| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.16 r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22020 Z= 0.099 Angle : 0.484 14.728 29708 Z= 0.247 Chirality : 0.039 0.186 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.693 17.650 2859 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 1.52 % Allowed : 19.38 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2583 helix: 2.08 (0.14), residues: 1493 sheet: -1.36 (0.39), residues: 156 loop : -1.05 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 143 HIS 0.003 0.001 HIS B 978 PHE 0.038 0.001 PHE B 636 TYR 0.018 0.001 TYR C 223 ARG 0.005 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 1090) hydrogen bonds : angle 3.61105 ( 3120) covalent geometry : bond 0.00226 (22020) covalent geometry : angle 0.48446 (29708) ********************** 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 220 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8202 (mtp85) REVERT: B 326 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8776 (ptt180) REVERT: B 337 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7871 (t0) REVERT: B 1001 MET cc_start: 0.9122 (mmm) cc_final: 0.8747 (mmm) REVERT: A 14 LYS cc_start: 0.7135 (tptt) cc_final: 0.6834 (tptt) REVERT: A 109 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: A 841 LEU cc_start: 0.8966 (mt) cc_final: 0.8686 (mp) REVERT: C 297 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: D 290 MET cc_start: 0.7882 (ppp) cc_final: 0.7438 (tmm) REVERT: E 28 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7788 (mm-30) REVERT: E 41 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8526 (pptt) outliers start: 36 outliers final: 24 residues processed: 213 average time/residue: 0.3532 time to fit residues: 119.3267 Evaluate side-chains 207 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 2.544 ------------------------------------------------------------------------------- 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 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 A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS 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 203 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 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 13 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 229 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 115 ASN C 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077537 restraints weight = 48176.191| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.12 r_work: 0.3060 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22020 Z= 0.091 Angle : 0.487 14.713 29708 Z= 0.247 Chirality : 0.038 0.184 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.606 17.974 2859 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.35 % Allowed : 19.55 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2583 helix: 2.14 (0.14), residues: 1490 sheet: -1.28 (0.39), residues: 156 loop : -0.98 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 143 HIS 0.003 0.000 HIS B 978 PHE 0.021 0.001 PHE A 500 TYR 0.021 0.001 TYR C 190 ARG 0.005 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 1090) hydrogen bonds : angle 3.55978 ( 3120) covalent geometry : bond 0.00203 (22020) covalent geometry : angle 0.48707 (29708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10407.05 seconds wall clock time: 182 minutes 16.69 seconds (10936.69 seconds total)