Starting phenix.real_space_refine on Tue Jan 21 05:18:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylt_39390/01_2025/8ylt_39390_trim.cif" } resolution = 3.09 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= 0.011 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 128 5.16 5 C 21536 2.51 5 N 5386 2.21 5 O 6268 1.98 5 H 32508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65834 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "B" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "C" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "D" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.98, per 1000 atoms: 0.35 Number of scatterers: 65834 At special positions: 0 Unit cell: (115.568, 128.616, 273.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 8 15.00 O 6268 8.00 N 5386 7.00 C 21536 6.00 H 32508 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 3.9 seconds 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 9 sheets defined 72.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.616A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.503A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.150A pdb=" N VAL A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.878A 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 155 through 160 removed outlier: 4.233A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.622A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.741A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.697A 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 334 removed outlier: 3.840A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.619A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 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 468 through 494 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.582A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.923A 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 637 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 701 removed outlier: 3.758A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.832A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.507A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 788 removed outlier: 4.206A pdb=" N ASP A 788 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.678A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.533A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) 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 903 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.788A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.617A pdb=" N HIS A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.823A 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: 3.924A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.725A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.567A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (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: 3.549A pdb=" N LEU B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.701A 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 366 through 373 removed outlier: 3.610A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.593A pdb=" N ASP B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 466 removed outlier: 3.935A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 495 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.330A 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 542 through 547 removed outlier: 4.018A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 547' Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.686A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 removed outlier: 3.718A pdb=" N GLU B 568 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.518A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.801A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 788 removed outlier: 3.651A pdb=" N ILE B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 788 " --> pdb=" O GLU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.670A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 removed outlier: 3.587A pdb=" N SER B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.812A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 903 Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.508A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 956 through 962 removed outlier: 3.943A pdb=" N LYS B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 991 removed outlier: 3.946A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.546A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 22 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 47 through 53 removed outlier: 4.346A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 3.883A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 removed outlier: 3.897A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 7.025A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.974A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.570A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.481A pdb=" N LYS C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.614A pdb=" N ASN C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 183 " --> pdb=" O GLY C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.605A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.947A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.612A pdb=" N LEU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.532A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.557A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.564A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.523A pdb=" N ARG C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 392 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 494 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 508 through 519 removed outlier: 3.518A pdb=" N MET C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.553A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN C 548 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 550 " --> pdb=" O ASP C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 572 Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.507A pdb=" N LEU C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.943A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 629 removed outlier: 3.598A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 629 " --> pdb=" O TYR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.658A pdb=" N SER C 637 " --> pdb=" O GLU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 701 removed outlier: 4.628A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.500A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 760 Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 800 through 812 removed outlier: 3.765A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 827 Processing helix chain 'C' and resid 832 through 840 Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'C' and resid 846 through 857 Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 878 through 903 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 934 removed outlier: 3.893A pdb=" N ILE C 934 " --> pdb=" O GLU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 950 through 954 removed outlier: 3.527A pdb=" N LYS C 953 " --> pdb=" O ASP C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 956 No H-bonds generated for 'chain 'C' and resid 955 through 956' Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.902A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 962 " --> pdb=" O TRP C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 962' Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 973 through 991 removed outlier: 4.750A pdb=" N HIS C 978 " --> pdb=" O LYS C 974 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1003 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.602A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.506A pdb=" N LYS D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.731A pdb=" N TRP D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.605A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 281 through 298 removed outlier: 3.952A pdb=" N LEU D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.522A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.733A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.567A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 466 removed outlier: 3.613A pdb=" N ILE D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 495 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.746A pdb=" N MET D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.154A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 removed outlier: 3.551A pdb=" N THR D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 564 through 569 removed outlier: 4.070A pdb=" N GLU D 568 " --> pdb=" O LYS D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.795A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.583A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 680 through 701 removed outlier: 3.523A pdb=" N ILE D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 701 " --> pdb=" O LYS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 4.203A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.853A pdb=" N PHE D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 762 removed outlier: 3.524A pdb=" N LEU D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.525A pdb=" N HIS D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.631A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.647A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 861 through 871 Processing helix chain 'D' and resid 878 through 903 Processing helix chain 'D' and resid 911 through 922 removed outlier: 3.794A pdb=" N THR D 915 " --> pdb=" O ASP D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 932 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 961 Processing helix chain 'D' and resid 963 through 973 Processing helix chain 'D' and resid 976 through 991 Processing helix chain 'D' and resid 993 through 1003 removed outlier: 3.579A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.602A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.511A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 4.187A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.365A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 44 " --> pdb=" O HIS C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.656A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 44 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 338 through 340 1853 hydrogen bonds defined for protein. 5364 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: 23.48 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 32468 1.01 - 1.21: 159 1.21 - 1.42: 14663 1.42 - 1.62: 19118 1.62 - 1.82: 216 Bond restraints: 66624 Sorted by residual: bond pdb=" SG CYS C 142 " pdb=" HG CYS C 142 " ideal model delta sigma weight residual 1.200 1.342 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" SG CYS D 142 " pdb=" HG CYS D 142 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" SG CYS C 29 " pdb=" HG CYS C 29 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" SG CYS D 469 " pdb=" HG CYS D 469 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" SG CYS A 142 " pdb=" HG CYS A 142 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.96e+01 ... (remaining 66619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 113696 2.33 - 4.66: 6057 4.66 - 6.99: 189 6.99 - 9.32: 32 9.32 - 11.65: 6 Bond angle restraints: 119980 Sorted by residual: angle pdb=" N GLN B 297 " pdb=" CA GLN B 297 " pdb=" C GLN B 297 " ideal model delta sigma weight residual 111.14 102.00 9.14 1.08e+00 8.57e-01 7.16e+01 angle pdb=" N VAL B 18 " pdb=" CA VAL B 18 " pdb=" C VAL B 18 " ideal model delta sigma weight residual 110.42 102.74 7.68 9.60e-01 1.09e+00 6.39e+01 angle pdb=" N THR A 52 " pdb=" CA THR A 52 " pdb=" C THR A 52 " ideal model delta sigma weight residual 113.23 104.38 8.85 1.24e+00 6.50e-01 5.10e+01 angle pdb=" N GLY B 219 " pdb=" CA GLY B 219 " pdb=" C GLY B 219 " ideal model delta sigma weight residual 112.51 100.86 11.65 1.71e+00 3.42e-01 4.64e+01 angle pdb=" N PHE B 19 " pdb=" CA PHE B 19 " pdb=" C PHE B 19 " ideal model delta sigma weight residual 110.50 101.25 9.25 1.41e+00 5.03e-01 4.31e+01 ... (remaining 119975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 28317 17.92 - 35.84: 2191 35.84 - 53.76: 674 53.76 - 71.68: 217 71.68 - 89.61: 47 Dihedral angle restraints: 31446 sinusoidal: 16706 harmonic: 14740 Sorted by residual: dihedral pdb=" CA LEU B 767 " pdb=" C LEU B 767 " pdb=" N PRO B 768 " pdb=" CA PRO B 768 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 659 " pdb=" C PHE A 659 " pdb=" N LYS A 660 " pdb=" CA LYS A 660 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS B 902 " pdb=" C LYS B 902 " pdb=" N GLY B 903 " pdb=" CA GLY B 903 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 31443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3703 0.044 - 0.087: 851 0.087 - 0.131: 241 0.131 - 0.174: 49 0.174 - 0.218: 16 Chirality restraints: 4860 Sorted by residual: chirality pdb=" CA ILE D 138 " pdb=" N ILE D 138 " pdb=" C ILE D 138 " pdb=" CB ILE D 138 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE A 620 " pdb=" N ILE A 620 " pdb=" C ILE A 620 " pdb=" CB ILE A 620 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU A 767 " pdb=" N LEU A 767 " pdb=" C LEU A 767 " pdb=" CB LEU A 767 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4857 not shown) Planarity restraints: 9750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 563 " -0.083 2.00e-02 2.50e+03 4.87e-01 3.55e+03 pdb=" CG ASN B 563 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 563 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B 563 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 563 " -0.841 2.00e-02 2.50e+03 pdb="HD22 ASN B 563 " 0.838 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 477 " -0.227 2.00e-02 2.50e+03 4.67e-01 3.28e+03 pdb=" CG ASN C 477 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 477 " 0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN C 477 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 477 " 0.770 2.00e-02 2.50e+03 pdb="HD22 ASN C 477 " -0.785 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 115 " -0.308 2.00e-02 2.50e+03 4.30e-01 2.77e+03 pdb=" CG ASN D 115 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN D 115 " 0.290 2.00e-02 2.50e+03 pdb=" ND2 ASN D 115 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN D 115 " 0.669 2.00e-02 2.50e+03 pdb="HD22 ASN D 115 " -0.693 2.00e-02 2.50e+03 ... (remaining 9747 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 642 2.05 - 2.69: 105345 2.69 - 3.33: 202541 3.33 - 3.96: 254464 3.96 - 4.60: 400274 Nonbonded interactions: 963266 Sorted by model distance: nonbonded pdb=" HG1 THR A 824 " pdb=" HB1 ALA A 849 " model vdw 1.418 2.270 nonbonded pdb=" HG1 THR D 824 " pdb=" HB1 ALA D 849 " model vdw 1.536 2.270 nonbonded pdb="HG21 VAL A 489 " pdb="HD21 LEU A 512 " model vdw 1.564 2.440 nonbonded pdb=" HG SER D 366 " pdb=" OE1 GLU D 369 " model vdw 1.604 2.450 nonbonded pdb=" O GLU D 560 " pdb="HH12 ARG D 566 " model vdw 1.616 2.450 ... (remaining 963261 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1005 or resid 1101)) selection = chain 'C' selection = (chain 'D' and (resid 14 through 1005 or resid 1101)) } 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: 5.370 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: 0.840 Extract box with map and model: 1.850 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 106.400 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.007 0.078 34116 Z= 0.452 Angle : 0.891 11.654 45984 Z= 0.579 Chirality : 0.044 0.218 4860 Planarity : 0.004 0.059 5852 Dihedral : 15.905 89.606 12872 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.90 % Allowed : 11.88 % Favored : 87.21 % 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: 0.18 (0.13), residues: 3970 helix: 0.68 (0.10), residues: 2494 sheet: -3.69 (0.57), residues: 52 loop : -0.59 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.008 0.001 HIS A 349 PHE 0.038 0.001 PHE B1004 TYR 0.024 0.002 TYR D 260 ARG 0.007 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 298 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: C 21 MET cc_start: 0.6148 (ttp) cc_final: 0.5865 (tpt) REVERT: C 155 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6838 (mm-30) REVERT: C 290 MET cc_start: 0.8458 (tpt) cc_final: 0.8105 (tpt) REVERT: D 37 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.7467 (m) REVERT: D 290 MET cc_start: 0.8679 (tpp) cc_final: 0.7801 (tpp) outliers start: 33 outliers final: 11 residues processed: 212 average time/residue: 0.9406 time to fit residues: 318.1475 Evaluate side-chains 157 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 6.9990 chunk 300 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 263 ASN A 614 ASN B 115 ASN B 192 ASN B 563 ASN B 910 ASN B 926 ASN C 39 ASN C 58 GLN C 297 GLN C 598 ASN C 614 ASN D 202 ASN D 867 ASN D 895 ASN D 926 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.199053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105906 restraints weight = 178480.174| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 10.55 r_work: 0.3120 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work: 0.3249 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34116 Z= 0.172 Angle : 0.502 6.715 45984 Z= 0.275 Chirality : 0.037 0.176 4860 Planarity : 0.003 0.053 5852 Dihedral : 6.605 75.232 4642 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.68 % Allowed : 12.51 % Favored : 86.80 % 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: 0.60 (0.13), residues: 3970 helix: 1.06 (0.10), residues: 2566 sheet: -3.04 (0.72), residues: 40 loop : -0.67 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 143 HIS 0.004 0.001 HIS A 349 PHE 0.018 0.001 PHE B 178 TYR 0.020 0.001 TYR D 11 ARG 0.003 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8488 (mp0) cc_final: 0.8198 (mp0) REVERT: B 104 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 21 MET cc_start: 0.5904 (ttp) cc_final: 0.5517 (tpt) REVERT: C 274 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8274 (mp) outliers start: 25 outliers final: 13 residues processed: 178 average time/residue: 0.8918 time to fit residues: 263.7603 Evaluate side-chains 154 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 375 optimal weight: 40.0000 chunk 395 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 335 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 306 optimal weight: 0.8980 chunk 259 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 992 ASN D 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.198456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106509 restraints weight = 157316.308| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 6.93 r_work: 0.3147 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 34116 Z= 0.286 Angle : 0.483 9.092 45984 Z= 0.268 Chirality : 0.037 0.145 4860 Planarity : 0.003 0.055 5852 Dihedral : 5.877 67.155 4629 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.71 % Allowed : 12.65 % Favored : 86.64 % 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: 0.79 (0.13), residues: 3970 helix: 1.29 (0.10), residues: 2554 sheet: -3.19 (0.71), residues: 42 loop : -0.75 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.008 0.001 HIS B 881 PHE 0.025 0.001 PHE C 107 TYR 0.021 0.001 TYR A 589 ARG 0.004 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 PHE cc_start: 0.8021 (t80) cc_final: 0.7413 (t80) REVERT: B 104 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8894 (mp) REVERT: B 866 MET cc_start: 0.9034 (ppp) cc_final: 0.8758 (ppp) REVERT: C 21 MET cc_start: 0.6238 (ttp) cc_final: 0.5648 (tpt) REVERT: C 274 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8433 (mp) REVERT: D 98 MET cc_start: 0.8596 (ttp) cc_final: 0.8118 (tmm) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 0.8822 time to fit residues: 242.5457 Evaluate side-chains 154 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 348 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 371 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 297 GLN B 78 ASN B 428 GLN B 521 ASN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104438 restraints weight = 175222.234| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 10.18 r_work: 0.3063 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34116 Z= 0.219 Angle : 0.445 5.801 45984 Z= 0.246 Chirality : 0.036 0.154 4860 Planarity : 0.003 0.052 5852 Dihedral : 5.656 66.611 4627 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.93 % Allowed : 12.81 % Favored : 86.25 % 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: 1.00 (0.13), residues: 3970 helix: 1.47 (0.10), residues: 2560 sheet: -3.27 (0.72), residues: 42 loop : -0.71 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 143 HIS 0.005 0.001 HIS B 171 PHE 0.026 0.001 PHE A 107 TYR 0.015 0.001 TYR A 324 ARG 0.003 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: B 104 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 298 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: B 976 MET cc_start: 0.7746 (mtm) cc_final: 0.7517 (ptp) REVERT: C 21 MET cc_start: 0.6186 (ttp) cc_final: 0.5750 (tpt) REVERT: D 98 MET cc_start: 0.8780 (ttp) cc_final: 0.8302 (tmm) REVERT: D 204 MET cc_start: 0.9379 (ttp) cc_final: 0.9023 (ttp) outliers start: 34 outliers final: 20 residues processed: 166 average time/residue: 0.8465 time to fit residues: 230.9329 Evaluate side-chains 156 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 126 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 283 optimal weight: 30.0000 chunk 308 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 141 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.201109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103562 restraints weight = 172885.455| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 9.59 r_work: 0.3037 rms_B_bonded: 6.59 restraints_weight: 2.0000 r_work: 0.3171 rms_B_bonded: 5.56 restraints_weight: 4.0000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 34116 Z= 0.255 Angle : 0.447 6.474 45984 Z= 0.247 Chirality : 0.036 0.148 4860 Planarity : 0.003 0.058 5852 Dihedral : 5.635 67.959 4627 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.82 % Allowed : 12.90 % Favored : 86.28 % 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 (0.13), residues: 3970 helix: 1.56 (0.10), residues: 2548 sheet: -3.35 (0.72), residues: 42 loop : -0.70 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.004 0.001 HIS B 171 PHE 0.015 0.001 PHE A 107 TYR 0.013 0.001 TYR A 755 ARG 0.003 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: B 104 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (mp) REVERT: B 298 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: B 866 MET cc_start: 0.8934 (ppp) cc_final: 0.8688 (ppp) REVERT: C 21 MET cc_start: 0.6045 (ttp) cc_final: 0.5694 (tpt) REVERT: D 98 MET cc_start: 0.8499 (ttp) cc_final: 0.8130 (tmm) REVERT: D 204 MET cc_start: 0.9259 (ttp) cc_final: 0.8793 (ttp) outliers start: 30 outliers final: 21 residues processed: 158 average time/residue: 0.8924 time to fit residues: 231.2776 Evaluate side-chains 158 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 246 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 chunk 163 optimal weight: 0.2980 chunk 367 optimal weight: 0.9990 chunk 284 optimal weight: 20.0000 chunk 105 optimal weight: 0.0270 chunk 337 optimal weight: 8.9990 chunk 121 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 289 optimal weight: 0.0670 chunk 260 optimal weight: 0.9980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN B 992 ASN D 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.205610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123797 restraints weight = 195628.187| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 8.06 r_work: 0.3074 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34116 Z= 0.117 Angle : 0.408 6.747 45984 Z= 0.222 Chirality : 0.035 0.149 4860 Planarity : 0.002 0.053 5852 Dihedral : 5.392 68.122 4627 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.68 % Allowed : 12.90 % Favored : 86.42 % 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: 1.36 (0.14), residues: 3970 helix: 1.76 (0.11), residues: 2552 sheet: -3.29 (0.72), residues: 42 loop : -0.57 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 143 HIS 0.003 0.001 HIS A 415 PHE 0.016 0.001 PHE B 533 TYR 0.015 0.001 TYR A 912 ARG 0.005 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: A 124 MET cc_start: 0.9122 (mmm) cc_final: 0.8623 (mmm) REVERT: B 104 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8950 (mp) REVERT: B 298 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: B 866 MET cc_start: 0.9001 (ppp) cc_final: 0.8697 (ppp) REVERT: B 976 MET cc_start: 0.7812 (mtm) cc_final: 0.7551 (ptp) REVERT: C 21 MET cc_start: 0.6134 (ttp) cc_final: 0.5675 (tpt) REVERT: C 235 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8639 (mt) REVERT: C 274 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 98 MET cc_start: 0.8748 (ttp) cc_final: 0.8377 (tmm) REVERT: D 204 MET cc_start: 0.9408 (ttp) cc_final: 0.8989 (ttp) outliers start: 25 outliers final: 19 residues processed: 158 average time/residue: 0.8426 time to fit residues: 220.5824 Evaluate side-chains 156 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 205 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.203218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114523 restraints weight = 196001.465| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 10.22 r_work: 0.3028 rms_B_bonded: 6.76 restraints_weight: 2.0000 r_work: 0.3151 rms_B_bonded: 5.90 restraints_weight: 4.0000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 34116 Z= 0.287 Angle : 0.453 6.860 45984 Z= 0.249 Chirality : 0.036 0.146 4860 Planarity : 0.003 0.051 5852 Dihedral : 5.414 68.963 4623 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.85 % Allowed : 12.90 % Favored : 86.25 % 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: 1.30 (0.13), residues: 3970 helix: 1.74 (0.11), residues: 2552 sheet: -3.36 (0.74), residues: 42 loop : -0.63 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 143 HIS 0.005 0.001 HIS B 67 PHE 0.013 0.001 PHE A 811 TYR 0.014 0.001 TYR A 324 ARG 0.004 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 ASP cc_start: 0.8866 (m-30) cc_final: 0.8437 (m-30) REVERT: B 298 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: B 866 MET cc_start: 0.9042 (ppp) cc_final: 0.8787 (ppp) REVERT: B 976 MET cc_start: 0.7279 (mtm) cc_final: 0.7065 (ptp) REVERT: C 21 MET cc_start: 0.6037 (ttp) cc_final: 0.5699 (tpt) REVERT: C 274 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8539 (mp) REVERT: D 98 MET cc_start: 0.8648 (ttp) cc_final: 0.8332 (tmm) REVERT: D 204 MET cc_start: 0.9299 (ttp) cc_final: 0.8835 (ttp) REVERT: D 290 MET cc_start: 0.8971 (mmm) cc_final: 0.8715 (mmm) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 0.8393 time to fit residues: 221.7711 Evaluate side-chains 158 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 163 optimal weight: 0.1980 chunk 324 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 393 optimal weight: 30.0000 chunk 147 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.204863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125090 restraints weight = 201098.255| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 9.25 r_work: 0.3079 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34116 Z= 0.154 Angle : 0.413 7.012 45984 Z= 0.225 Chirality : 0.035 0.147 4860 Planarity : 0.002 0.050 5852 Dihedral : 5.190 68.618 4621 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.68 % Allowed : 13.03 % Favored : 86.28 % 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: 1.46 (0.14), residues: 3970 helix: 1.85 (0.11), residues: 2552 sheet: -3.34 (0.73), residues: 42 loop : -0.54 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 143 HIS 0.003 0.001 HIS C 978 PHE 0.016 0.001 PHE B 533 TYR 0.014 0.001 TYR A 324 ARG 0.002 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 MET cc_start: 0.5993 (mpp) cc_final: 0.5722 (mpp) REVERT: B 298 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: B 976 MET cc_start: 0.7901 (mtm) cc_final: 0.7588 (ptp) REVERT: C 21 MET cc_start: 0.6272 (ttp) cc_final: 0.5767 (tpt) REVERT: C 235 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8647 (mt) REVERT: C 274 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 98 MET cc_start: 0.8778 (ttp) cc_final: 0.8464 (tmm) REVERT: D 204 MET cc_start: 0.9373 (ttp) cc_final: 0.8966 (ttp) outliers start: 25 outliers final: 21 residues processed: 156 average time/residue: 0.8302 time to fit residues: 215.1676 Evaluate side-chains 158 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 386 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 364 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 330 optimal weight: 40.0000 chunk 221 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 381 optimal weight: 30.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 549 GLN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.202715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122800 restraints weight = 194866.265| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 9.48 r_work: 0.3062 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work: 0.3062 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0625 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0312 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0156 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0078 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0039 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0020 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0010 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0005 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0002 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0001 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0001 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work: 0.3035 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 34116 Z= 0.322 Angle : 0.461 7.285 45984 Z= 0.255 Chirality : 0.037 0.147 4860 Planarity : 0.003 0.049 5852 Dihedral : 5.348 69.429 4621 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.85 % Allowed : 12.98 % Favored : 86.17 % 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: 1.30 (0.13), residues: 3970 helix: 1.74 (0.10), residues: 2554 sheet: -3.48 (0.72), residues: 42 loop : -0.63 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 143 HIS 0.006 0.001 HIS B 171 PHE 0.015 0.001 PHE A 646 TYR 0.021 0.001 TYR A 324 ARG 0.004 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 MET cc_start: 0.6692 (mpp) cc_final: 0.6364 (mpp) REVERT: B 298 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: C 21 MET cc_start: 0.6326 (ttp) cc_final: 0.5767 (tpt) REVERT: C 274 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 98 MET cc_start: 0.8781 (ttp) cc_final: 0.8467 (tmm) REVERT: D 204 MET cc_start: 0.9402 (ttp) cc_final: 0.9009 (ttp) outliers start: 31 outliers final: 23 residues processed: 157 average time/residue: 0.8490 time to fit residues: 221.8030 Evaluate side-chains 158 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 170 optimal weight: 1.9990 chunk 211 optimal weight: 0.3980 chunk 271 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 321 optimal weight: 0.0970 chunk 380 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 992 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.205106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116874 restraints weight = 200208.312| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 7.98 r_work: 0.3087 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34116 Z= 0.128 Angle : 0.411 8.052 45984 Z= 0.224 Chirality : 0.035 0.149 4860 Planarity : 0.002 0.048 5852 Dihedral : 5.144 68.672 4621 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.52 % Allowed : 13.31 % Favored : 86.17 % 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: 1.53 (0.14), residues: 3970 helix: 1.89 (0.11), residues: 2552 sheet: -3.40 (0.72), residues: 42 loop : -0.48 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 143 HIS 0.003 0.001 HIS A 658 PHE 0.016 0.001 PHE B 533 TYR 0.019 0.001 TYR A 324 ARG 0.003 0.000 ARG C 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7940 Ramachandran restraints generated. 3970 Oldfield, 0 Emsley, 3970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: C 21 MET cc_start: 0.6275 (ttp) cc_final: 0.5853 (tpt) REVERT: C 235 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8617 (mt) REVERT: C 274 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 98 MET cc_start: 0.8736 (ttp) cc_final: 0.8465 (tmm) REVERT: D 204 MET cc_start: 0.9354 (ttp) cc_final: 0.8988 (ttp) outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 0.8457 time to fit residues: 207.9733 Evaluate side-chains 153 residues out of total 3652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 765 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 976 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 49 optimal weight: 0.7980 chunk 287 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 345 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.203402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120205 restraints weight = 199388.166| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 9.49 r_work: 0.3018 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work: 0.3128 rms_B_bonded: 5.17 restraints_weight: 4.0000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34116 Z= 0.266 Angle : 0.442 7.919 45984 Z= 0.243 Chirality : 0.036 0.146 4860 Planarity : 0.002 0.047 5852 Dihedral : 5.229 69.517 4621 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.66 % Allowed : 13.25 % Favored : 86.09 % 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: 1.48 (0.14), residues: 3970 helix: 1.86 (0.11), residues: 2542 sheet: -3.46 (0.73), residues: 42 loop : -0.49 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 143 HIS 0.005 0.001 HIS B 171 PHE 0.015 0.001 PHE B1004 TYR 0.021 0.001 TYR A 324 ARG 0.004 0.000 ARG B 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 59952.22 seconds wall clock time: 1016 minutes 30.76 seconds (60990.76 seconds total)