Starting phenix.real_space_refine on Tue Jul 23 07:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/07_2024/8wkn_37603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/07_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_37603/07_2024/8wkn_37603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/07_2024/8wkn_37603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/07_2024/8wkn_37603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkn_37603/07_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.86, per 1000 atoms: 0.55 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: 8.44 Conformation dependent library (CDL) restraints added in 4.3 seconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4966 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 12 sheets defined 65.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 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: 7.33 Time building geometry restraints manager: 9.25 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 2.440 nonbonded pdb=" OG SER A 80 " pdb=" OD1 ASP A 82 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASN A 927 " pdb=" N LYS A 929 " model vdw 2.222 2.520 nonbonded pdb=" OE1 GLU B 341 " pdb=" OG1 THR B 345 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR E 16 " pdb=" OD1 ASN E 21 " model vdw 2.227 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 504 or (resid 505 and \ (name N or name CA or name C or name O or name CB )) or resid 506 through 637 or \ (resid 638 through 639 and (name N or name CA or name C or name O or name CB )) \ or resid 640 through 747 or resid 749 through 896 or resid 910 through 934 or r \ esid 936 through 1005)) selection = (chain 'B' and (resid 22 through 566 or resid 578 through 787 or resid 789 throu \ gh 896 or resid 910 through 911 or (resid 912 and (name N or name CA or name C o \ r name O or name CB )) or resid 913 through 974 or resid 976 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 23 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB )) or resid 106 through 299)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 58.150 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.220 ------------------------------------------------------------------------------- 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 : 2.712 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: 0.3385 time to fit residues: 101.0995 Evaluate side-chains 180 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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: 10.0000 chunk 196 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 0.0670 chunk 235 optimal weight: 9.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS A 867 ASN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22020 Z= 0.262 Angle : 0.512 10.241 29708 Z= 0.269 Chirality : 0.040 0.150 3180 Planarity : 0.004 0.053 3797 Dihedral : 4.214 57.574 2870 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 1.86 % Allowed : 18.83 % Favored : 79.31 % 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: 0.79 (0.17), residues: 2583 helix: 1.80 (0.14), residues: 1489 sheet: -1.60 (0.39), residues: 147 loop : -1.22 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 A 436 ARG 0.004 0.000 ARG D 175 *********************** 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 231 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.732 Fit side-chains revert: symmetry clash REVERT: B 521 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8264 (p0) REVERT: A 134 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7994 (p90) REVERT: A 892 ARG cc_start: 0.9059 (ttm110) cc_final: 0.8722 (mtp-110) REVERT: C 190 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7458 (t80) REVERT: C 223 TYR cc_start: 0.7092 (t80) cc_final: 0.6067 (t80) REVERT: E 69 GLU cc_start: 0.8599 (mp0) cc_final: 0.8336 (mp0) outliers start: 44 outliers final: 16 residues processed: 220 average time/residue: 0.3601 time to fit residues: 124.9163 Evaluate side-chains 196 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 980 VAL 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: 0.0980 chunk 195 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 D 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1015 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= 0.257 Angle : 0.498 10.744 29708 Z= 0.260 Chirality : 0.040 0.155 3180 Planarity : 0.004 0.054 3797 Dihedral : 3.959 19.158 2859 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.94 % Allowed : 19.26 % 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: 0.83 (0.17), residues: 2583 helix: 1.87 (0.14), residues: 1489 sheet: -1.47 (0.40), residues: 142 loop : -1.29 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 143 HIS 0.004 0.001 HIS B 241 PHE 0.019 0.001 PHE B 636 TYR 0.012 0.001 TYR A 436 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: 46 poor density : 181 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8298 (mtp85) REVERT: B 326 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8786 (ptt180) REVERT: B 521 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8278 (p0) REVERT: B 1001 MET cc_start: 0.9152 (mmm) cc_final: 0.8662 (mmm) REVERT: A 237 LYS cc_start: 0.8780 (tppt) cc_final: 0.8563 (tppt) REVERT: A 892 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8767 (mtp-110) REVERT: D 23 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5876 (t0) REVERT: E 69 GLU cc_start: 0.8644 (mp0) cc_final: 0.8392 (mp0) outliers start: 46 outliers final: 28 residues processed: 214 average time/residue: 0.3367 time to fit residues: 112.0639 Evaluate side-chains 202 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 278 ASN 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 492 PHE Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 555 THR 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 674 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP 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 139 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 236 optimal weight: 0.4980 chunk 250 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 939 GLN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22020 Z= 0.209 Angle : 0.475 11.660 29708 Z= 0.248 Chirality : 0.039 0.144 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.921 18.686 2859 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 2.28 % Allowed : 18.96 % Favored : 78.76 % 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: 0.92 (0.17), residues: 2583 helix: 1.92 (0.14), residues: 1501 sheet: -1.47 (0.40), residues: 142 loop : -1.26 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.021 0.001 PHE B 636 TYR 0.011 0.001 TYR A 471 ARG 0.002 0.000 ARG B 285 *********************** 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 : 2.397 Fit side-chains revert: symmetry clash REVERT: B 326 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8784 (ptt180) REVERT: B 630 ASP cc_start: 0.6694 (t0) cc_final: 0.6470 (t0) REVERT: A 892 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8720 (mtp-110) REVERT: A 998 GLU cc_start: 0.8774 (tt0) cc_final: 0.8427 (tt0) REVERT: C 75 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6970 (ttpp) REVERT: C 223 TYR cc_start: 0.7574 (t80) cc_final: 0.7300 (t80) REVERT: E 69 GLU cc_start: 0.8718 (mp0) cc_final: 0.8459 (mp0) outliers start: 54 outliers final: 28 residues processed: 229 average time/residue: 0.3218 time to fit residues: 115.7195 Evaluate side-chains 205 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 278 ASN Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 980 VAL 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 674 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1001 MET 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 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 939 GLN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22020 Z= 0.367 Angle : 0.547 12.323 29708 Z= 0.284 Chirality : 0.041 0.146 3180 Planarity : 0.004 0.053 3797 Dihedral : 4.096 19.150 2859 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 2.83 % Allowed : 19.17 % Favored : 78.00 % 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: 0.74 (0.17), residues: 2583 helix: 1.78 (0.14), residues: 1494 sheet: -1.43 (0.39), residues: 152 loop : -1.32 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 757 HIS 0.004 0.001 HIS B 241 PHE 0.017 0.001 PHE A 533 TYR 0.014 0.001 TYR B 755 ARG 0.003 0.000 ARG A 613 *********************** 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 238 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 2.588 Fit side-chains REVERT: B 175 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8251 (mtp85) REVERT: B 326 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8906 (ptt180) REVERT: B 521 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8288 (p0) REVERT: B 630 ASP cc_start: 0.6759 (t0) cc_final: 0.6524 (t0) REVERT: A 109 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: A 998 GLU cc_start: 0.8829 (tt0) cc_final: 0.8478 (tt0) REVERT: C 223 TYR cc_start: 0.7788 (t80) cc_final: 0.7456 (t80) outliers start: 67 outliers final: 43 residues processed: 222 average time/residue: 0.3251 time to fit residues: 114.1677 Evaluate side-chains 216 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 278 ASN 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 492 PHE Chi-restraints excluded: chain B residue 521 ASN 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 234 LYS Chi-restraints excluded: chain A residue 316 ILE 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 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP 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 D residue 296 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22020 Z= 0.304 Angle : 0.520 13.225 29708 Z= 0.269 Chirality : 0.040 0.155 3180 Planarity : 0.004 0.054 3797 Dihedral : 4.087 18.813 2859 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 3.08 % Allowed : 19.34 % Favored : 77.58 % 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: 0.76 (0.17), residues: 2583 helix: 1.80 (0.14), residues: 1497 sheet: -1.49 (0.38), residues: 152 loop : -1.32 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 143 HIS 0.004 0.001 HIS C 211 PHE 0.016 0.001 PHE A 533 TYR 0.013 0.001 TYR A 436 ARG 0.003 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 174 time to evaluate : 2.565 Fit side-chains REVERT: B 175 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8274 (mtp85) REVERT: B 326 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8880 (ptt180) REVERT: B 630 ASP cc_start: 0.6796 (t0) cc_final: 0.6554 (t0) REVERT: A 109 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: A 998 GLU cc_start: 0.8796 (tt0) cc_final: 0.8443 (tt0) REVERT: C 109 GLN cc_start: 0.9272 (tp40) cc_final: 0.9012 (tp-100) REVERT: C 115 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 175 ARG cc_start: 0.8847 (mtp-110) cc_final: 0.8621 (mtm110) outliers start: 73 outliers final: 52 residues processed: 228 average time/residue: 0.3163 time to fit residues: 114.1578 Evaluate side-chains 227 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 278 ASN 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 402 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 749 LEU 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 234 LYS Chi-restraints excluded: chain A residue 316 ILE 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 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP 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 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 139 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22020 Z= 0.136 Angle : 0.463 13.587 29708 Z= 0.240 Chirality : 0.038 0.154 3180 Planarity : 0.003 0.052 3797 Dihedral : 3.876 17.704 2859 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.98 % Allowed : 20.40 % Favored : 77.62 % 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: 1.03 (0.17), residues: 2583 helix: 2.00 (0.14), residues: 1501 sheet: -1.45 (0.38), residues: 154 loop : -1.17 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.013 0.001 PHE A 837 TYR 0.012 0.001 TYR A 471 ARG 0.003 0.000 ARG B 285 *********************** 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 234 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 2.395 Fit side-chains REVERT: B 175 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8268 (mtp85) REVERT: B 326 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8739 (ptt180) REVERT: A 109 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: A 998 GLU cc_start: 0.8740 (tt0) cc_final: 0.8406 (tt0) REVERT: C 115 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7000 (t0) REVERT: C 190 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8246 (t80) REVERT: D 175 ARG cc_start: 0.8844 (mtp-110) cc_final: 0.8614 (mtm110) outliers start: 47 outliers final: 31 residues processed: 222 average time/residue: 0.3480 time to fit residues: 122.9588 Evaluate side-chains 214 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 2.552 ------------------------------------------------------------------------------- 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 278 ASN Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1001 MET 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 182 ASN 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 D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 296 SER 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: 2.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 123 optimal weight: 0.0470 chunk 23 optimal weight: 0.0770 chunk 196 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 939 GLN C 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22020 Z= 0.127 Angle : 0.468 14.502 29708 Z= 0.240 Chirality : 0.038 0.173 3180 Planarity : 0.003 0.051 3797 Dihedral : 3.726 17.052 2859 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 1.94 % Allowed : 20.78 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2583 helix: 2.11 (0.14), residues: 1501 sheet: -1.37 (0.38), residues: 154 loop : -1.12 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 143 HIS 0.009 0.001 HIS A 503 PHE 0.038 0.001 PHE A 492 TYR 0.013 0.001 TYR D 261 ARG 0.005 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 233 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 2.602 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: B 188 ASP cc_start: 0.8616 (m-30) cc_final: 0.8349 (m-30) REVERT: B 326 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8764 (ptt180) REVERT: A 998 GLU cc_start: 0.8703 (tt0) cc_final: 0.8371 (tt0) REVERT: C 115 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7091 (t0) REVERT: C 190 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (t80) REVERT: D 175 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8642 (mtm110) outliers start: 46 outliers final: 31 residues processed: 219 average time/residue: 0.3274 time to fit residues: 113.0165 Evaluate side-chains 211 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 278 ASN Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1001 MET 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 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 D residue 296 SER Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 109 GLN A 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22020 Z= 0.271 Angle : 0.519 14.423 29708 Z= 0.266 Chirality : 0.040 0.179 3180 Planarity : 0.004 0.055 3797 Dihedral : 3.836 17.221 2859 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.07 % Allowed : 20.65 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2583 helix: 2.05 (0.14), residues: 1496 sheet: -1.47 (0.38), residues: 154 loop : -1.18 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 143 HIS 0.005 0.001 HIS A 979 PHE 0.025 0.001 PHE A 500 TYR 0.011 0.001 TYR A 552 ARG 0.004 0.000 ARG B 285 *********************** 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 228 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 2.725 Fit side-chains REVERT: B 175 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8269 (mtp85) REVERT: B 326 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8834 (ptt180) REVERT: B 521 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8318 (p0) REVERT: A 998 GLU cc_start: 0.8779 (tt0) cc_final: 0.8463 (tt0) REVERT: C 115 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7399 (t0) REVERT: C 190 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8196 (t80) REVERT: C 223 TYR cc_start: 0.7926 (t80) cc_final: 0.7259 (t80) REVERT: D 175 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8641 (mtm110) REVERT: D 290 MET cc_start: 0.7962 (ppp) cc_final: 0.7660 (ppp) outliers start: 49 outliers final: 38 residues processed: 217 average time/residue: 0.3333 time to fit residues: 113.5892 Evaluate side-chains 218 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1001 MET 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 182 ASN 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 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 233 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 296 SER 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 Chi-restraints excluded: chain E residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.1980 chunk 245 optimal weight: 10.0000 chunk 150 optimal weight: 0.0770 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 109 GLN A 939 GLN C 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22020 Z= 0.124 Angle : 0.480 14.784 29708 Z= 0.246 Chirality : 0.038 0.183 3180 Planarity : 0.003 0.053 3797 Dihedral : 3.732 16.980 2859 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 1.65 % Allowed : 21.16 % Favored : 77.20 % 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: 1.18 (0.17), residues: 2583 helix: 2.14 (0.14), residues: 1496 sheet: -1.40 (0.38), residues: 154 loop : -1.13 (0.20), residues: 933 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 0.042 0.001 PHE B 636 TYR 0.011 0.001 TYR A 193 ARG 0.007 0.000 ARG C 86 ********************** 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 221 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: B 175 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: B 326 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8747 (ptt180) REVERT: A 504 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 841 LEU cc_start: 0.8951 (mt) cc_final: 0.8669 (mp) REVERT: A 998 GLU cc_start: 0.8726 (tt0) cc_final: 0.8417 (tt0) REVERT: C 115 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7261 (t0) REVERT: C 190 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8183 (t80) REVERT: C 223 TYR cc_start: 0.7745 (t80) cc_final: 0.7056 (t80) REVERT: C 278 ASN cc_start: 0.9124 (m110) cc_final: 0.8632 (p0) REVERT: C 290 MET cc_start: 0.8961 (mmm) cc_final: 0.8746 (mmm) REVERT: D 175 ARG cc_start: 0.8863 (mtp-110) cc_final: 0.8638 (mtm110) REVERT: D 290 MET cc_start: 0.7928 (ppp) cc_final: 0.7611 (ppp) outliers start: 39 outliers final: 29 residues processed: 209 average time/residue: 0.3381 time to fit residues: 110.8091 Evaluate side-chains 213 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 2.595 ------------------------------------------------------------------------------- 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 373 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1001 MET 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 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 233 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 296 SER 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: 0.9990 chunk 218 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.107594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075969 restraints weight = 48313.307| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.14 r_work: 0.3027 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22020 Z= 0.140 Angle : 0.476 14.665 29708 Z= 0.243 Chirality : 0.038 0.184 3180 Planarity : 0.003 0.054 3797 Dihedral : 3.663 16.727 2859 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 1.60 % Allowed : 21.07 % Favored : 77.32 % 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: 1.22 (0.17), residues: 2583 helix: 2.17 (0.14), residues: 1500 sheet: -1.35 (0.38), residues: 154 loop : -1.11 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 143 HIS 0.003 0.001 HIS A 978 PHE 0.027 0.001 PHE A 492 TYR 0.010 0.001 TYR D 261 ARG 0.007 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.43 seconds wall clock time: 74 minutes 8.06 seconds (4448.06 seconds total)