Starting phenix.real_space_refine on Wed Aug 7 22:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wye_37925/08_2024/8wye_37925.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.087 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 78 5.16 5 C 13748 2.51 5 N 3432 2.21 5 O 3974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 945": "OD1" <-> "OD2" Residue "A TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 964": "OD1" <-> "OD2" Residue "B GLU 982": "OE1" <-> "OE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21232 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7895 Classifications: {'peptide': 945} Link IDs: {'PTRANS': 19, 'TRANS': 925} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "C" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2195 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "E" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Time building chain proxies: 12.34, per 1000 atoms: 0.58 Number of scatterers: 21232 At special positions: 0 Unit cell: (98.413, 126.531, 180.286, 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 78 16.00 O 3974 8.00 N 3432 7.00 C 13748 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: 8.19 Conformation dependent library (CDL) restraints added in 3.7 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 9 sheets defined 67.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.956A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.907A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.600A 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 179 through 183 removed outlier: 3.610A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.521A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) 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 235 removed outlier: 3.580A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.540A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.532A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.723A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 372' Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 495 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.607A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.635A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.991A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.849A 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 743 Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 768 through 787 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.658A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.789A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.602A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) 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 973 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.946A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.804A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.533A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.627A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.252A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.774A 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 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.869A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.647A 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 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.670A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.569A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 495 removed outlier: 3.546A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 524 through 530 removed outlier: 4.442A pdb=" N PHE B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.241A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.555A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.837A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.734A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.808A 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 743 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.541A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.937A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.688A pdb=" N ILE B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.685A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 895 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 930 through 934 removed outlier: 3.574A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 955 through 961 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 992 Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.523A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.074A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.707A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.782A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.907A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 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 235 removed outlier: 3.536A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.739A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.020A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.607A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 removed outlier: 4.055A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.857A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 297 removed outlier: 3.657A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.151A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.943A pdb=" N PHE C 23 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.179A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 72 removed outlier: 7.271A pdb=" N GLU C 38 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU C 33 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN C 40 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE C 31 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE C 44 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL C 27 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU C 28 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA C 86 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP C 30 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 71 through 72 removed outlier: 10.185A pdb=" N GLU C 115 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE C 44 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL C 117 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 46 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.047A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.175A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 9.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6721 1.34 - 1.46: 5244 1.46 - 1.58: 9637 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 21731 Sorted by residual: bond pdb=" CG1 ILE E 33 " pdb=" CD1 ILE E 33 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.86e+00 bond pdb=" CG1 ILE E 30 " pdb=" CD1 ILE E 30 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CB LYS B 237 " pdb=" CG LYS B 237 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CB GLU A 379 " pdb=" CG GLU A 379 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CG GLU A 379 " pdb=" CD GLU A 379 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 21726 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 254 105.35 - 112.54: 10726 112.54 - 119.73: 7520 119.73 - 126.92: 10623 126.92 - 134.11: 195 Bond angle restraints: 29318 Sorted by residual: angle pdb=" C ILE B 835 " pdb=" N ASP B 836 " pdb=" CA ASP B 836 " ideal model delta sigma weight residual 121.58 113.91 7.67 1.95e+00 2.63e-01 1.55e+01 angle pdb=" CA ILE E 33 " pdb=" CB ILE E 33 " pdb=" CG1 ILE E 33 " ideal model delta sigma weight residual 110.40 115.98 -5.58 1.70e+00 3.46e-01 1.08e+01 angle pdb=" N ILE E 33 " pdb=" CA ILE E 33 " pdb=" CB ILE E 33 " ideal model delta sigma weight residual 110.54 114.91 -4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" C LYS D 237 " pdb=" N ASP D 238 " pdb=" CA ASP D 238 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.67e+00 angle pdb=" CB LYS B 237 " pdb=" CG LYS B 237 " pdb=" CD LYS B 237 " ideal model delta sigma weight residual 111.30 118.43 -7.13 2.30e+00 1.89e-01 9.60e+00 ... (remaining 29313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10812 17.83 - 35.66: 1538 35.66 - 53.49: 451 53.49 - 71.32: 90 71.32 - 89.16: 27 Dihedral angle restraints: 12918 sinusoidal: 5341 harmonic: 7577 Sorted by residual: dihedral pdb=" CA LYS C 19 " pdb=" C LYS C 19 " pdb=" N ILE C 20 " pdb=" CA ILE C 20 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR B 338 " pdb=" C TYR B 338 " pdb=" N HIS B 339 " pdb=" CA HIS B 339 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 12915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2304 0.040 - 0.080: 631 0.080 - 0.120: 179 0.120 - 0.160: 14 0.160 - 0.199: 4 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB ILE E 33 " pdb=" CA ILE E 33 " pdb=" CG1 ILE E 33 " pdb=" CG2 ILE E 33 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CG LEU A 922 " pdb=" CB LEU A 922 " pdb=" CD1 LEU A 922 " pdb=" CD2 LEU A 922 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CB ILE B 751 " pdb=" CA ILE B 751 " pdb=" CG1 ILE B 751 " pdb=" CG2 ILE B 751 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3129 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 249 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" CG ASP E 249 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 249 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 249 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 945 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CG ASP A 945 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 945 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 945 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 531 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 532 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " 0.024 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 276 2.62 - 3.19: 18519 3.19 - 3.76: 34946 3.76 - 4.33: 50284 4.33 - 4.90: 81420 Nonbonded interactions: 185445 Sorted by model distance: nonbonded pdb=" O TYR A 313 " pdb=" OG SER A 317 " model vdw 2.044 3.040 nonbonded pdb=" O VAL A 470 " pdb=" OG SER A 474 " model vdw 2.096 3.040 nonbonded pdb=" OG SER B 366 " pdb=" OE1 GLU B 369 " model vdw 2.125 3.040 nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 2.130 3.040 nonbonded pdb=" OH TYR B 324 " pdb=" OD1 ASP B 590 " model vdw 2.135 3.040 ... (remaining 185440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 26 through 297) } 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: 11.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 57.950 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.003 0.077 21731 Z= 0.206 Angle : 0.518 8.848 29318 Z= 0.279 Chirality : 0.040 0.199 3132 Planarity : 0.003 0.044 3732 Dihedral : 18.235 89.156 8044 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.05 % Allowed : 27.46 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2517 helix: 1.16 (0.13), residues: 1525 sheet: -0.17 (0.56), residues: 63 loop : -0.14 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.021 0.001 PHE A 921 TYR 0.023 0.001 TYR A 951 ARG 0.007 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 282 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 ASP cc_start: 0.7649 (t0) cc_final: 0.7209 (m-30) outliers start: 95 outliers final: 86 residues processed: 370 average time/residue: 1.1384 time to fit residues: 488.8105 Evaluate side-chains 358 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 272 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 591 ASN A 765 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 521 ASN B 548 ASN B 711 GLN B 765 ASN B 832 GLN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 226 ASN D 297 GLN E 128 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21731 Z= 0.311 Angle : 0.539 9.189 29318 Z= 0.287 Chirality : 0.042 0.274 3132 Planarity : 0.004 0.042 3732 Dihedral : 7.659 75.150 2956 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.52 % Allowed : 24.61 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 2517 helix: 1.24 (0.13), residues: 1526 sheet: -0.88 (0.52), residues: 63 loop : 0.03 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.017 0.002 PHE B 646 TYR 0.021 0.002 TYR A 951 ARG 0.004 0.001 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 308 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6487 (ttm-80) REVERT: B 454 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8120 (tp) REVERT: B 673 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7841 (mm) outliers start: 106 outliers final: 41 residues processed: 396 average time/residue: 1.2058 time to fit residues: 550.4124 Evaluate side-chains 328 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 711 GLN A 765 ASN A 797 ASN B 202 ASN B 467 ASN B 548 ASN B 765 ASN B 848 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 128 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21731 Z= 0.232 Angle : 0.493 7.304 29318 Z= 0.264 Chirality : 0.040 0.154 3132 Planarity : 0.003 0.042 3732 Dihedral : 6.213 74.335 2860 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.56 % Allowed : 23.54 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2517 helix: 1.30 (0.13), residues: 1525 sheet: -1.24 (0.52), residues: 63 loop : 0.00 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.014 0.001 PHE B 699 TYR 0.013 0.001 TYR B 166 ARG 0.006 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 312 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8428 (mmt) REVERT: A 840 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7822 (mttp) REVERT: A 938 ASP cc_start: 0.8042 (m-30) cc_final: 0.7823 (m-30) REVERT: B 53 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7618 (mp) REVERT: B 379 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: B 454 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8030 (tp) REVERT: B 463 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5120 (pt) REVERT: B 517 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7383 (ttp-110) REVERT: B 673 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7742 (mm) REVERT: B 930 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6925 (mtp) REVERT: D 58 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: D 97 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7122 (tt0) outliers start: 107 outliers final: 39 residues processed: 396 average time/residue: 1.2090 time to fit residues: 549.7762 Evaluate side-chains 331 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 281 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 765 ASN B 202 ASN B 410 ASN B 467 ASN B 548 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21731 Z= 0.345 Angle : 0.544 12.064 29318 Z= 0.287 Chirality : 0.043 0.210 3132 Planarity : 0.004 0.041 3732 Dihedral : 5.746 78.580 2843 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.95 % Allowed : 23.16 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2517 helix: 1.16 (0.13), residues: 1523 sheet: -1.48 (0.52), residues: 63 loop : -0.01 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.017 0.002 PHE B 699 TYR 0.016 0.002 TYR B 912 ARG 0.006 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 292 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8610 (mmt) REVERT: A 840 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7906 (mttp) REVERT: A 938 ASP cc_start: 0.8064 (m-30) cc_final: 0.7849 (m-30) REVERT: B 53 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 379 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: B 454 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 463 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5180 (pt) REVERT: B 517 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7407 (ttp-110) REVERT: B 673 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7884 (mm) REVERT: D 58 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: D 97 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7105 (tt0) outliers start: 116 outliers final: 50 residues processed: 385 average time/residue: 1.1754 time to fit residues: 521.0342 Evaluate side-chains 340 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 280 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 182 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 169 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN A 797 ASN B 202 ASN B 467 ASN B 521 ASN B 548 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21731 Z= 0.171 Angle : 0.477 7.419 29318 Z= 0.255 Chirality : 0.039 0.147 3132 Planarity : 0.003 0.042 3732 Dihedral : 5.491 80.810 2842 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.97 % Allowed : 23.88 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2517 helix: 1.37 (0.13), residues: 1532 sheet: -1.48 (0.50), residues: 75 loop : -0.03 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.012 0.001 PHE B 699 TYR 0.015 0.001 TYR A 951 ARG 0.007 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 299 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8380 (mmt) REVERT: A 711 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: B 53 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7530 (mp) REVERT: B 97 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: B 454 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7997 (tp) REVERT: B 467 ASN cc_start: 0.6607 (OUTLIER) cc_final: 0.6254 (p0) REVERT: B 517 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7357 (ttp-110) REVERT: B 673 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7746 (mm) REVERT: B 930 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6861 (mtp) REVERT: D 97 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7027 (tt0) outliers start: 93 outliers final: 36 residues processed: 372 average time/residue: 1.2291 time to fit residues: 525.6148 Evaluate side-chains 326 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN B 202 ASN B 467 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21731 Z= 0.222 Angle : 0.500 8.683 29318 Z= 0.264 Chirality : 0.040 0.261 3132 Planarity : 0.003 0.041 3732 Dihedral : 5.206 87.099 2830 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.88 % Allowed : 24.22 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2517 helix: 1.38 (0.13), residues: 1532 sheet: -1.50 (0.51), residues: 75 loop : -0.02 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.014 0.001 PHE B 699 TYR 0.019 0.001 TYR A 951 ARG 0.006 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 289 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8383 (mmt) REVERT: A 711 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: A 840 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7798 (mttp) REVERT: B 53 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7539 (mp) REVERT: B 97 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: B 379 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6908 (pt0) REVERT: B 454 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8041 (tp) REVERT: B 517 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7467 (ttp-110) REVERT: B 673 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7742 (mm) REVERT: B 930 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6969 (mtp) REVERT: D 97 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7006 (tt0) outliers start: 91 outliers final: 43 residues processed: 360 average time/residue: 1.2301 time to fit residues: 507.9075 Evaluate side-chains 333 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 206 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN A 810 HIS B 202 ASN B 467 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21731 Z= 0.202 Angle : 0.506 9.368 29318 Z= 0.266 Chirality : 0.040 0.194 3132 Planarity : 0.003 0.040 3732 Dihedral : 5.118 86.375 2827 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.67 % Allowed : 24.78 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2517 helix: 1.41 (0.13), residues: 1532 sheet: -1.49 (0.51), residues: 75 loop : -0.03 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.009 0.001 HIS B 339 PHE 0.013 0.001 PHE B 699 TYR 0.020 0.001 TYR A 951 ARG 0.009 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 297 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7765 (mttp) REVERT: B 53 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 97 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6474 (tt0) REVERT: B 379 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: B 454 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8004 (tp) REVERT: B 517 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7511 (ttp-110) REVERT: B 673 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7750 (mm) outliers start: 86 outliers final: 41 residues processed: 362 average time/residue: 1.2174 time to fit residues: 506.5555 Evaluate side-chains 327 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 279 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 0.0570 chunk 22 optimal weight: 0.2980 chunk 191 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 810 HIS B 202 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21731 Z= 0.166 Angle : 0.494 9.335 29318 Z= 0.258 Chirality : 0.039 0.161 3132 Planarity : 0.003 0.039 3732 Dihedral : 4.620 49.761 2824 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.90 % Allowed : 25.97 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2517 helix: 1.52 (0.13), residues: 1533 sheet: -1.46 (0.50), residues: 75 loop : -0.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 121 HIS 0.008 0.001 HIS B 339 PHE 0.011 0.001 PHE B 699 TYR 0.018 0.001 TYR A 951 ARG 0.008 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 312 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7705 (mttp) REVERT: B 454 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8021 (tp) REVERT: B 517 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7431 (ttp-110) REVERT: B 673 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7735 (mm) REVERT: E 227 MET cc_start: 0.7045 (tpp) cc_final: 0.6844 (mmp) outliers start: 68 outliers final: 31 residues processed: 364 average time/residue: 1.2314 time to fit residues: 512.7783 Evaluate side-chains 317 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 205 optimal weight: 0.0770 chunk 214 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN A 810 HIS B 202 ASN B 467 ASN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21731 Z= 0.242 Angle : 0.539 11.336 29318 Z= 0.280 Chirality : 0.041 0.277 3132 Planarity : 0.003 0.039 3732 Dihedral : 4.639 48.625 2821 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.77 % Allowed : 26.18 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2517 helix: 1.44 (0.13), residues: 1533 sheet: -1.50 (0.50), residues: 75 loop : -0.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 757 HIS 0.010 0.001 HIS B 339 PHE 0.015 0.001 PHE B 699 TYR 0.020 0.001 TYR A 951 ARG 0.008 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7799 (mttp) REVERT: B 454 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8051 (tp) REVERT: B 517 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7466 (ttp-110) REVERT: B 673 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7770 (mm) REVERT: E 227 MET cc_start: 0.7215 (tpp) cc_final: 0.6990 (mmp) outliers start: 65 outliers final: 33 residues processed: 340 average time/residue: 1.1995 time to fit residues: 472.5990 Evaluate side-chains 314 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 765 ASN B 202 ASN B 467 ASN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 21731 Z= 0.253 Angle : 0.692 59.190 29318 Z= 0.390 Chirality : 0.041 0.297 3132 Planarity : 0.004 0.068 3732 Dihedral : 4.662 48.626 2821 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.30 % Allowed : 26.82 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2517 helix: 1.43 (0.13), residues: 1533 sheet: -1.51 (0.50), residues: 75 loop : -0.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.015 0.001 PHE B 699 TYR 0.017 0.001 TYR A 951 ARG 0.011 0.000 ARG E 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 276 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7797 (mttp) REVERT: B 379 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: B 454 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8048 (tp) REVERT: B 517 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7392 (ttp-110) REVERT: B 673 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7769 (mm) outliers start: 54 outliers final: 37 residues processed: 317 average time/residue: 1.2312 time to fit residues: 447.6110 Evaluate side-chains 321 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 279 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 206 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 765 ASN B 202 ASN B 765 ASN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114840 restraints weight = 24804.548| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.16 r_work: 0.3442 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 21731 Z= 0.253 Angle : 0.692 59.190 29318 Z= 0.390 Chirality : 0.041 0.297 3132 Planarity : 0.004 0.068 3732 Dihedral : 4.662 48.626 2821 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 27.29 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2517 helix: 1.43 (0.13), residues: 1533 sheet: -1.51 (0.50), residues: 75 loop : -0.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 PHE 0.015 0.001 PHE B 699 TYR 0.017 0.001 TYR A 951 ARG 0.011 0.000 ARG E 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8795.68 seconds wall clock time: 156 minutes 38.88 seconds (9398.88 seconds total)