Starting phenix.real_space_refine on Thu Aug 8 01:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_37603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_37603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_37603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_37603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/08_2024/8wkn_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 Residue "B ASP 238": "OD1" <-> "OD2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.82, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 4.5 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: 3.05 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: 7.71 Time building geometry restraints manager: 9.79 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: 80.77 - 94.14: 2 94.14 - 107.51: 480 107.51 - 120.88: 22973 120.88 - 134.24: 6251 134.24 - 147.61: 2 Bond angle restraints: 29708 Sorted by residual: angle pdb=" O GLY C 177 " pdb=" C GLY C 177 " pdb=" N LYS C 179 " ideal model delta sigma weight residual 122.70 80.77 41.93 1.30e+00 5.92e-01 1.04e+03 angle pdb=" O GLY D 177 " pdb=" C GLY D 177 " pdb=" N LYS D 179 " ideal model delta sigma weight residual 122.70 86.55 36.15 1.30e+00 5.92e-01 7.73e+02 angle pdb=" O ILE B 934 " pdb=" C ILE B 934 " pdb=" N MET B 936 " ideal model delta sigma weight residual 123.20 94.33 28.87 1.06e+00 8.90e-01 7.42e+02 angle pdb=" C ILE B 934 " pdb=" N MET B 936 " pdb=" CA MET B 936 " ideal model delta sigma weight residual 121.54 147.61 -26.07 1.91e+00 2.74e-01 1.86e+02 angle pdb=" C GLY D 177 " pdb=" N LYS D 179 " pdb=" CA LYS D 179 " ideal model delta sigma weight residual 121.54 141.99 -20.45 1.91e+00 2.74e-01 1.15e+02 ... (remaining 29703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11275 17.75 - 35.50: 1465 35.50 - 53.26: 319 53.26 - 71.01: 51 71.01 - 88.76: 11 Dihedral angle restraints: 13121 sinusoidal: 5395 harmonic: 7726 Sorted by residual: dihedral pdb=" CA ILE B 934 " pdb=" C ILE B 934 " pdb=" N MET B 936 " pdb=" CA MET B 936 " ideal model delta harmonic sigma weight residual 180.00 -93.53 -86.47 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA GLY C 177 " pdb=" C GLY C 177 " pdb=" N LYS C 179 " pdb=" CA LYS C 179 " ideal model delta harmonic sigma weight residual 180.00 145.49 34.51 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ALA E 60 " pdb=" C ALA E 60 " pdb=" N VAL E 61 " pdb=" CA VAL E 61 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 13118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2297 0.040 - 0.079: 698 0.079 - 0.119: 165 0.119 - 0.158: 16 0.158 - 0.198: 4 Chirality restraints: 3180 Sorted by residual: chirality pdb=" CA ASN C 125 " pdb=" N ASN C 125 " pdb=" C ASN C 125 " pdb=" CB ASN C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA ILE B 934 " pdb=" N ILE B 934 " pdb=" C ILE B 934 " pdb=" CB ILE B 934 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA LYS C 176 " pdb=" N LYS C 176 " pdb=" C LYS C 176 " pdb=" CB LYS C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 3177 not shown) Planarity restraints: 3797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 177 " 0.192 2.00e-02 2.50e+03 2.75e-01 7.56e+02 pdb=" C GLY C 177 " -0.461 2.00e-02 2.50e+03 pdb=" O GLY C 177 " 0.226 2.00e-02 2.50e+03 pdb=" N LYS C 179 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 177 " 0.174 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C GLY D 177 " -0.413 2.00e-02 2.50e+03 pdb=" O GLY D 177 " 0.179 2.00e-02 2.50e+03 pdb=" N LYS D 179 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 934 " 0.150 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C ILE B 934 " -0.370 2.00e-02 2.50e+03 pdb=" O ILE B 934 " 0.158 2.00e-02 2.50e+03 pdb=" N MET B 936 " 0.063 2.00e-02 2.50e+03 ... (remaining 3794 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2872 2.75 - 3.29: 20802 3.29 - 3.83: 34833 3.83 - 4.36: 38974 4.36 - 4.90: 69144 Nonbonded interactions: 166625 Sorted by model distance: nonbonded pdb=" OH TYR B 71 " pdb=" OG1 THR C 257 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 80 " pdb=" OD1 ASP A 82 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 927 " pdb=" N LYS A 929 " model vdw 2.222 3.120 nonbonded pdb=" OE1 GLU B 341 " pdb=" OG1 THR B 345 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR E 16 " pdb=" OD1 ASN E 21 " model vdw 2.227 3.040 ... (remaining 166620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 504 or (resid 505 and \ (name N or name CA or name C or name O or name CB )) or resid 506 through 637 or \ (resid 638 through 639 and (name N or name CA or name C or name O or name CB )) \ or resid 640 through 747 or resid 749 through 896 or resid 910 through 934 or r \ esid 936 through 1005)) selection = (chain 'B' and (resid 22 through 566 or resid 578 through 787 or resid 789 throu \ gh 896 or resid 910 through 911 or (resid 912 and (name N or name CA or name C o \ r name O or name CB )) or resid 913 through 974 or resid 976 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 23 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB )) or resid 106 through 299)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 62.720 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.220 ------------------------------------------------------------------------------- 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= 0.899 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 2.613 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: 0.3373 time to fit residues: 100.1327 Evaluate side-chains 180 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 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= 0.314 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 *********************** 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 fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 2.522 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7978 (p90) REVERT: A 892 ARG cc_start: 0.9060 (ttm110) cc_final: 0.8722 (mtp-110) REVERT: C 190 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7538 (t80) REVERT: C 223 TYR cc_start: 0.7290 (t80) cc_final: 0.6419 (t80) REVERT: C 247 ARG cc_start: 0.6849 (ttt180) cc_final: 0.6371 (ttt180) outliers start: 42 outliers final: 19 residues processed: 221 average time/residue: 0.3590 time to fit residues: 122.6037 Evaluate side-chains 195 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1070 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= 0.186 Angle : 0.482 10.757 29708 Z= 0.253 Chirality : 0.039 0.155 3180 Planarity : 0.004 0.054 3797 Dihedral : 3.918 18.735 2859 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 1.65 % Allowed : 18.33 % Favored : 80.03 % 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 E 88 PHE 0.020 0.001 PHE B 636 TYR 0.012 0.001 TYR D 286 ARG 0.003 0.000 ARG D 175 *********************** 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 227 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8170 (mtp85) REVERT: B 326 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8808 (ptt180) REVERT: B 1001 MET cc_start: 0.9119 (mmm) cc_final: 0.8682 (mmm) REVERT: A 134 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7980 (p90) REVERT: A 892 ARG cc_start: 0.9076 (ttm110) cc_final: 0.8755 (mtp-110) REVERT: A 998 GLU cc_start: 0.8800 (tt0) cc_final: 0.8585 (tt0) REVERT: C 247 ARG cc_start: 0.6955 (ttt180) cc_final: 0.6500 (ttt180) outliers start: 39 outliers final: 19 residues processed: 215 average time/residue: 0.3322 time to fit residues: 109.7314 Evaluate side-chains 197 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 232 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 236 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 C 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22020 Z= 0.258 Angle : 0.510 11.542 29708 Z= 0.265 Chirality : 0.040 0.151 3180 Planarity : 0.004 0.053 3797 Dihedral : 3.928 18.820 2859 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 2.28 % Allowed : 18.03 % Favored : 79.69 % 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: -1.53 (0.40), residues: 142 loop : -1.22 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 143 HIS 0.004 0.001 HIS B 241 PHE 0.020 0.001 PHE B 636 TYR 0.012 0.001 TYR B 755 ARG 0.003 0.000 ARG D 175 *********************** 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 238 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 2.838 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8192 (mtp85) REVERT: B 326 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8825 (ptt180) REVERT: A 134 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7951 (p90) REVERT: A 237 LYS cc_start: 0.8751 (tppt) cc_final: 0.8538 (tppt) REVERT: A 291 ASP cc_start: 0.8905 (m-30) cc_final: 0.8648 (m-30) REVERT: A 892 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8705 (mtp-110) REVERT: C 75 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6954 (ttpp) REVERT: C 223 TYR cc_start: 0.7466 (t80) cc_final: 0.7237 (t80) REVERT: D 175 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8627 (mtp-110) REVERT: E 28 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7709 (mm-30) outliers start: 54 outliers final: 29 residues processed: 226 average time/residue: 0.3549 time to fit residues: 123.6496 Evaluate side-chains 207 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 ASP 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 234 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 224 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22020 Z= 0.244 Angle : 0.500 12.348 29708 Z= 0.259 Chirality : 0.040 0.148 3180 Planarity : 0.004 0.052 3797 Dihedral : 3.950 18.365 2859 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.24 % Allowed : 18.41 % Favored : 79.35 % 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: 0.88 (0.17), residues: 2583 helix: 1.86 (0.14), residues: 1494 sheet: -1.55 (0.40), residues: 142 loop : -1.19 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 143 HIS 0.003 0.001 HIS A 118 PHE 0.018 0.001 PHE B 636 TYR 0.012 0.001 TYR D 260 ARG 0.003 0.000 ARG A 165 *********************** 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 232 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 2.816 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8256 (mtp85) REVERT: B 326 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8812 (ptt180) REVERT: B 1001 MET cc_start: 0.9097 (mmm) cc_final: 0.8646 (mmm) REVERT: A 109 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: A 291 ASP cc_start: 0.8907 (m-30) cc_final: 0.8645 (m-30) REVERT: A 998 GLU cc_start: 0.8795 (tt0) cc_final: 0.8504 (tt0) REVERT: C 223 TYR cc_start: 0.7547 (t80) cc_final: 0.7217 (t80) REVERT: E 28 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7727 (mm-30) outliers start: 53 outliers final: 36 residues processed: 222 average time/residue: 0.3310 time to fit residues: 115.8164 Evaluate side-chains 211 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 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 C residue 228 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 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 84 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 250 optimal weight: 0.0870 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 131 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 HIS ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1471 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= 0.203 Angle : 0.485 13.166 29708 Z= 0.251 Chirality : 0.039 0.154 3180 Planarity : 0.003 0.051 3797 Dihedral : 3.892 17.762 2859 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.20 % Allowed : 18.62 % Favored : 79.18 % 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: 0.95 (0.17), residues: 2583 helix: 1.93 (0.14), residues: 1495 sheet: -1.47 (0.38), residues: 154 loop : -1.18 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.022 0.001 PHE A 500 TYR 0.011 0.001 TYR A 471 ARG 0.002 0.000 ARG A 657 *********************** 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 240 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.530 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8272 (mtp85) REVERT: B 326 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8783 (ptt180) REVERT: B 1001 MET cc_start: 0.9084 (mmm) cc_final: 0.8642 (mmm) REVERT: A 109 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8511 (mt0) REVERT: A 504 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: A 998 GLU cc_start: 0.8789 (tt0) cc_final: 0.8499 (tt0) REVERT: C 223 TYR cc_start: 0.7663 (t80) cc_final: 0.7171 (t80) outliers start: 52 outliers final: 36 residues processed: 229 average time/residue: 0.3270 time to fit residues: 117.8036 Evaluate side-chains 216 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL 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 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 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 228 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 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 241 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 415 HIS ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22020 Z= 0.222 Angle : 0.500 13.506 29708 Z= 0.258 Chirality : 0.039 0.155 3180 Planarity : 0.004 0.054 3797 Dihedral : 3.896 17.630 2859 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.32 % Allowed : 18.79 % Favored : 78.89 % 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: 0.96 (0.17), residues: 2583 helix: 1.93 (0.14), residues: 1495 sheet: -1.48 (0.38), residues: 154 loop : -1.16 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 143 HIS 0.003 0.001 HIS A 118 PHE 0.024 0.001 PHE B 354 TYR 0.011 0.001 TYR A 471 ARG 0.004 0.000 ARG D 145 *********************** 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 235 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 2.511 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8282 (mtp85) REVERT: B 326 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8808 (ptt180) REVERT: B 337 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 1001 MET cc_start: 0.9089 (mmm) cc_final: 0.8635 (mmm) REVERT: A 109 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: A 998 GLU cc_start: 0.8791 (tt0) cc_final: 0.8506 (tt0) REVERT: C 28 GLU cc_start: 0.9004 (mp0) cc_final: 0.8641 (mp0) REVERT: C 115 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.6996 (t0) outliers start: 55 outliers final: 43 residues processed: 223 average time/residue: 0.3503 time to fit residues: 123.0979 Evaluate side-chains 224 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 188 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 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 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 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 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 154 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22020 Z= 0.168 Angle : 0.489 14.377 29708 Z= 0.251 Chirality : 0.039 0.159 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.818 17.470 2859 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 2.15 % Allowed : 18.79 % Favored : 79.05 % 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: 2.01 (0.14), residues: 1491 sheet: -1.45 (0.38), residues: 154 loop : -1.12 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 143 HIS 0.008 0.001 HIS A 503 PHE 0.040 0.001 PHE A 492 TYR 0.011 0.001 TYR A 471 ARG 0.004 0.000 ARG D 145 *********************** 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 235 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8765 (ptt180) REVERT: B 337 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7821 (t0) REVERT: A 14 LYS cc_start: 0.6907 (tptt) cc_final: 0.6669 (tptt) REVERT: A 109 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: A 504 TYR cc_start: 0.7805 (m-80) cc_final: 0.7506 (m-80) REVERT: A 998 GLU cc_start: 0.8763 (tt0) cc_final: 0.8479 (tt0) REVERT: C 115 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7087 (t0) REVERT: C 290 MET cc_start: 0.8947 (mmm) cc_final: 0.8677 (mmm) REVERT: D 175 ARG cc_start: 0.8910 (mtp-110) cc_final: 0.8671 (mtm110) REVERT: D 290 MET cc_start: 0.8146 (ppp) cc_final: 0.7772 (ppp) outliers start: 51 outliers final: 34 residues processed: 226 average time/residue: 0.3220 time to fit residues: 115.1404 Evaluate side-chains 219 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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 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 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 228 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 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 227 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1688 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= 0.174 Angle : 0.488 14.489 29708 Z= 0.251 Chirality : 0.039 0.173 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.783 17.171 2859 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.90 % Allowed : 19.30 % Favored : 78.80 % 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: 1.08 (0.17), residues: 2583 helix: 2.02 (0.14), residues: 1494 sheet: -1.42 (0.38), residues: 154 loop : -1.09 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 143 HIS 0.003 0.001 HIS A 979 PHE 0.025 0.001 PHE A 492 TYR 0.013 0.001 TYR C 223 ARG 0.004 0.000 ARG D 145 *********************** 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 230 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 ASP cc_start: 0.8707 (m-30) cc_final: 0.8486 (m-30) REVERT: B 326 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8769 (ptt180) REVERT: B 337 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7800 (t0) REVERT: A 14 LYS cc_start: 0.6916 (tptt) cc_final: 0.6669 (tptt) REVERT: A 998 GLU cc_start: 0.8764 (tt0) cc_final: 0.8492 (tt0) REVERT: C 115 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7131 (t0) REVERT: C 190 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (t80) REVERT: C 290 MET cc_start: 0.8940 (mmm) cc_final: 0.8643 (mmm) REVERT: D 175 ARG cc_start: 0.8918 (mtp-110) cc_final: 0.8683 (mtm110) REVERT: D 290 MET cc_start: 0.8089 (ppp) cc_final: 0.7747 (ppp) outliers start: 45 outliers final: 37 residues processed: 221 average time/residue: 0.3219 time to fit residues: 113.0215 Evaluate side-chains 221 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 284 GLU 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 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 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 39 LEU Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 258 optimal weight: 0.3980 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22020 Z= 0.146 Angle : 0.481 14.618 29708 Z= 0.246 Chirality : 0.039 0.177 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.708 17.998 2859 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 1.73 % Allowed : 19.72 % Favored : 78.55 % 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: 1.17 (0.17), residues: 2583 helix: 2.11 (0.14), residues: 1488 sheet: -1.39 (0.38), residues: 154 loop : -1.05 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.039 0.001 PHE B 636 TYR 0.016 0.001 TYR C 223 ARG 0.005 0.000 ARG D 145 ********************** 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 228 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 ASP cc_start: 0.8700 (m-30) cc_final: 0.8492 (m-30) REVERT: B 326 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8793 (ptt180) REVERT: B 337 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7751 (t0) REVERT: A 14 LYS cc_start: 0.6907 (tptt) cc_final: 0.6663 (tptt) REVERT: A 504 TYR cc_start: 0.7742 (m-80) cc_final: 0.7495 (m-80) REVERT: A 998 GLU cc_start: 0.8714 (tt0) cc_final: 0.8442 (tt0) REVERT: C 115 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7153 (t0) REVERT: C 190 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8229 (t80) REVERT: C 280 TYR cc_start: 0.8048 (m-80) cc_final: 0.7802 (m-10) REVERT: C 290 MET cc_start: 0.8965 (mmm) cc_final: 0.8664 (mmm) REVERT: D 290 MET cc_start: 0.8125 (ppp) cc_final: 0.7709 (ppp) outliers start: 41 outliers final: 32 residues processed: 219 average time/residue: 0.3224 time to fit residues: 111.2138 Evaluate side-chains 215 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 284 GLU 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 316 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain 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 39 LEU Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 211 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.108139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076790 restraints weight = 48218.172| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.12 r_work: 0.3045 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1836 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= 0.128 Angle : 0.480 14.836 29708 Z= 0.246 Chirality : 0.038 0.176 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.644 19.242 2859 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 1.69 % Allowed : 19.85 % Favored : 78.46 % 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: 1.23 (0.17), residues: 2583 helix: 2.15 (0.14), residues: 1488 sheet: -1.34 (0.39), residues: 154 loop : -1.02 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.027 0.001 PHE A 492 TYR 0.016 0.001 TYR C 223 ARG 0.005 0.000 ARG D 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.01 seconds wall clock time: 75 minutes 55.17 seconds (4555.17 seconds total)