Starting phenix.real_space_refine on Sat Feb 7 17:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyb_37922/02_2026/8wyb_37922_neut.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.048 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 132 5.16 5 C 23014 2.51 5 N 5724 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7940 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7948 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "C" Number of atoms: 7915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7915 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 18, 'TRANS': 929} Chain breaks: 7 Chain: "D" Number of atoms: 7921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7921 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 19, 'TRANS': 929} Chain breaks: 7 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "F" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 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: 8.04, per 1000 atoms: 0.23 Number of scatterers: 35604 At special positions: 0 Unit cell: (100.067, 130.666, 258.851, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 8 15.00 O 6726 8.00 N 5724 7.00 C 23014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8140 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 14 sheets defined 65.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.556A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.035A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.535A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.798A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.505A pdb=" N ASP A 157 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.807A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.668A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.837A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.501A pdb=" N ARG A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.533A pdb=" N LYS A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.717A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 468 through 494 Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.536A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.153A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.169A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.819A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.178A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 801 through 813 removed outlier: 3.701A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.502A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.581A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 940 through 945 removed outlier: 3.526A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 removed outlier: 3.630A pdb=" N PHE A 949 " --> pdb=" O PRO A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 949' Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.163A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 974 removed outlier: 4.414A pdb=" N LYS A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 removed outlier: 3.830A pdb=" N VAL A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.128A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.599A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 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: 3.927A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.855A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.633A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.618A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.822A pdb=" N PHE B 301 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.534A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.761A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.553A pdb=" N ARG B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.612A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 501 removed outlier: 4.679A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.112A pdb=" N PHE B 528 " --> 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: 3.796A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.086A 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 572 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.550A pdb=" N GLU B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.566A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) 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 removed outlier: 4.107A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.240A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.731A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 813 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 840 through 845 Proline residue: B 843 - end of helix No H-bonds generated for 'chain 'B' and resid 840 through 845' Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.986A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.521A pdb=" N LEU B 865 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 940 through 945 Processing helix chain 'B' and resid 946 through 949 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 956 No H-bonds generated for 'chain 'B' and resid 955 through 956' Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.714A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 962 " --> pdb=" O TRP B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 962' Processing helix chain 'B' and resid 963 through 974 removed outlier: 4.524A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.577A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.652A pdb=" N GLU B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.794A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 82 through 108 Proline residue: C 88 - end of helix removed outlier: 7.152A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.574A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 235 removed outlier: 4.133A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 removed outlier: 3.543A pdb=" N ASN C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.748A pdb=" N ASP C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.517A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.807A pdb=" N ARG C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 431 through 445 removed outlier: 3.785A pdb=" N LYS C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 468 through 494 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.748A pdb=" N LEU C 498 " --> pdb=" O GLY C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.136A pdb=" N PHE C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 542 through 547 removed outlier: 3.638A pdb=" N SER C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 547' Processing helix chain 'C' and resid 551 through 572 Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.601A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 616 Processing helix chain 'C' and resid 618 through 628 Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 680 through 700 Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.914A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 765 removed outlier: 4.281A pdb=" N CYS C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 801 through 813 removed outlier: 3.577A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.801A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 removed outlier: 4.279A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 871 removed outlier: 3.584A pdb=" N LEU C 865 " --> pdb=" O ASN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 897 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 934 Processing helix chain 'C' and resid 940 through 945 removed outlier: 3.606A pdb=" N ASP C 945 " --> pdb=" O ASP C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 949 removed outlier: 3.649A pdb=" N PHE C 949 " --> pdb=" O PRO C 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 946 through 949' Processing helix chain 'C' and resid 950 through 954 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: 4.173A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.655A 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 972 Processing helix chain 'C' and resid 976 through 991 removed outlier: 3.715A pdb=" N VAL C 980 " --> pdb=" O MET C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1004 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.917A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.606A 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 96 through 109 removed outlier: 3.606A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.993A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 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 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.603A pdb=" N ILE D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 275' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.712A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.552A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.575A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 374 through 392 removed outlier: 3.750A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.534A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 495 removed outlier: 3.623A pdb=" N TYR D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 508 through 520 Processing helix chain 'D' and resid 525 through 530 removed outlier: 4.420A pdb=" N ASN D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 542 through 547 removed outlier: 3.571A pdb=" N SER D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 547 " --> pdb=" O GLU D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 547' Processing helix chain 'D' and resid 551 through 572 Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.532A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 616 Processing helix chain 'D' and resid 618 through 628 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: 4.164A pdb=" N ALA D 701 " --> pdb=" O LYS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.578A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.574A 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 742 Processing helix chain 'D' and resid 750 through 765 removed outlier: 4.424A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 813 removed outlier: 3.576A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 839 Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 857 removed outlier: 4.019A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 Processing helix chain 'D' and resid 878 through 897 Processing helix chain 'D' and resid 912 through 922 Processing helix chain 'D' and resid 929 through 934 Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 946 through 949 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 974 removed outlier: 4.405A pdb=" N LYS D 974 " --> pdb=" O ILE D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.750A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.585A pdb=" N GLU D 998 " --> pdb=" O LYS D 994 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'F' and resid 69 through 77 Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'H' and resid 69 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.287A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 574 through 575 current: chain 'E' and resid 21 through 32 removed outlier: 6.788A pdb=" N THR E 62 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA E 30 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E 60 " --> pdb=" O ALA E 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 63 current: chain 'E' and resid 192 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 906 through 908 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 906 through 908 current: chain 'F' and resid 21 through 35 removed outlier: 8.716A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE F 32 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN F 34 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 56 " --> pdb=" O GLN F 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 68 current: chain 'F' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 193 through 196 current: chain 'F' and resid 218 through 222 Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.932A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'B' and resid 794 through 795 removed outlier: 3.623A pdb=" N SER B 795 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.869A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 150 through 152 Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'C' and resid 574 through 575 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 574 through 575 current: chain 'G' and resid 21 through 32 removed outlier: 3.509A pdb=" N THR G 29 " --> pdb=" O THR G 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 63 current: chain 'G' and resid 192 through 195 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 192 through 195 current: chain 'G' and resid 218 through 222 Processing sheet with id=AB3, first strand: chain 'C' and resid 906 through 908 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 906 through 908 current: chain 'H' and resid 21 through 35 removed outlier: 8.122A pdb=" N VAL H 22 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE H 68 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR H 24 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA H 66 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR H 62 " --> pdb=" O GLN H 28 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA H 30 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN H 60 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE H 32 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU H 58 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN H 34 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU H 56 " --> pdb=" O GLN H 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 68 current: chain 'H' and resid 192 through 195 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 192 through 195 current: chain 'H' and resid 218 through 222 Processing sheet with id=AB4, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.337A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 340 1758 hydrogen bonds defined for protein. 5076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5990 1.32 - 1.44: 10180 1.44 - 1.57: 19991 1.57 - 1.69: 8 1.69 - 1.82: 228 Bond restraints: 36397 Sorted by residual: bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.503 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3 NAD D1101 " pdb=" PN NAD D1101 " ideal model delta sigma weight residual 1.633 1.501 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" O3 NAD D1101 " pdb=" PA NAD D1101 " ideal model delta sigma weight residual 1.653 1.541 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O3 NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 36392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.86: 48911 5.86 - 11.71: 107 11.71 - 17.57: 11 17.57 - 23.42: 1 23.42 - 29.28: 3 Bond angle restraints: 49033 Sorted by residual: angle pdb=" CA PRO A 956 " pdb=" N PRO A 956 " pdb=" CD PRO A 956 " ideal model delta sigma weight residual 112.00 96.44 15.56 1.40e+00 5.10e-01 1.24e+02 angle pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" O2B NAD B1101 " ideal model delta sigma weight residual 113.98 84.70 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" O2B NAD A1101 " ideal model delta sigma weight residual 113.98 84.71 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C1B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" O2B NAD C1101 " ideal model delta sigma weight residual 113.98 89.98 24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" CA PRO B 57 " pdb=" N PRO B 57 " pdb=" CD PRO B 57 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 ... (remaining 49028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 18606 20.13 - 40.26: 2558 40.26 - 60.38: 517 60.38 - 80.51: 91 80.51 - 100.64: 35 Dihedral angle restraints: 21807 sinusoidal: 9188 harmonic: 12619 Sorted by residual: dihedral pdb=" CA HIS C 349 " pdb=" C HIS C 349 " pdb=" N LYS C 350 " pdb=" CA LYS C 350 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA SER A 615 " pdb=" C SER A 615 " pdb=" N MET A 616 " pdb=" CA MET A 616 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU E 208 " pdb=" C LEU E 208 " pdb=" N GLU E 209 " pdb=" CA GLU E 209 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 21804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4910 0.084 - 0.167: 299 0.167 - 0.251: 20 0.251 - 0.335: 4 0.335 - 0.418: 2 Chirality restraints: 5235 Sorted by residual: chirality pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" N9A NAD A1101 " pdb=" O4B NAD A1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" N9A NAD B1101 " pdb=" O4B NAD B1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" C4B NAD C1101 " pdb=" O3B NAD C1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 5232 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 955 " 0.106 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO A 956 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 956 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 956 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 56 " 0.076 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 57 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 381 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 381 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 381 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 381 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 381 2.59 - 3.17: 31197 3.17 - 3.75: 58420 3.75 - 4.32: 80404 4.32 - 4.90: 132766 Nonbonded interactions: 303168 Sorted by model distance: nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 2.015 3.040 nonbonded pdb=" OD1 ASN A 78 " pdb=" N TYR A 79 " model vdw 2.068 3.120 nonbonded pdb=" OH TYR A 589 " pdb=" OD1 ASP A 651 " model vdw 2.103 3.040 nonbonded pdb=" OH TYR B 800 " pdb=" O ALA E 224 " model vdw 2.119 3.040 nonbonded pdb=" NZ LYS F 16 " pdb=" OD1 ASN F 197 " model vdw 2.158 3.120 ... (remaining 303163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 72 or resid 79 through 463 or resid 467 through \ 633 or resid 644 through 1101)) selection = (chain 'B' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1101)) selection = (chain 'C' and (resid 23 through 296 or resid 304 through 463 or resid 467 throu \ gh 633 or resid 644 through 1101)) selection = (chain 'D' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1101)) } ncs_group { reference = (chain 'E' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'F' and (resid 8 through 176 or resid 191 through 236)) selection = (chain 'G' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'H' and (resid 8 through 176 or resid 191 through 236)) } 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: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 32.000 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.005 0.159 36397 Z= 0.219 Angle : 0.818 29.279 49033 Z= 0.406 Chirality : 0.044 0.418 5235 Planarity : 0.004 0.147 6216 Dihedral : 18.623 100.641 13667 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.51 % Allowed : 29.35 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4155 helix: 0.61 (0.11), residues: 2423 sheet: -0.27 (0.34), residues: 190 loop : -1.07 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 380 TYR 0.048 0.002 TYR B 282 PHE 0.055 0.002 PHE C 381 TRP 0.026 0.002 TRP A 919 HIS 0.007 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00462 (36397) covalent geometry : angle 0.81805 (49033) hydrogen bonds : bond 0.14860 ( 1758) hydrogen bonds : angle 6.21387 ( 5076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 414 time to evaluate : 1.453 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: A 414 TYR cc_start: 0.7831 (t80) cc_final: 0.7499 (t80) REVERT: D 330 LEU cc_start: 0.8290 (tp) cc_final: 0.8085 (tt) REVERT: E 194 GLN cc_start: 0.5819 (tm-30) cc_final: 0.5587 (mp10) outliers start: 20 outliers final: 11 residues processed: 426 average time/residue: 0.2024 time to fit residues: 143.2547 Evaluate side-chains 394 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 383 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1003 TYR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain F residue 32 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 834 GLN B 351 ASN B 483 GLN B 765 ASN B 863 ASN C 39 ASN C 58 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN C 881 HIS D 226 ASN D 491 GLN D 521 ASN D 549 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN E 194 GLN E 197 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.225706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183663 restraints weight = 51275.784| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.91 r_work: 0.3663 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 36397 Z= 0.147 Angle : 0.596 9.274 49033 Z= 0.311 Chirality : 0.041 0.226 5235 Planarity : 0.004 0.078 6216 Dihedral : 8.508 85.535 4895 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 26.43 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4155 helix: 0.71 (0.10), residues: 2466 sheet: -0.61 (0.34), residues: 204 loop : -1.02 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 380 TYR 0.033 0.001 TYR D 418 PHE 0.024 0.002 PHE C 381 TRP 0.020 0.002 TRP D 601 HIS 0.008 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00338 (36397) covalent geometry : angle 0.59566 (49033) hydrogen bonds : bond 0.03945 ( 1758) hydrogen bonds : angle 4.84235 ( 5076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 431 time to evaluate : 1.086 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: A 414 TYR cc_start: 0.7788 (t80) cc_final: 0.7584 (t80) REVERT: B 134 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6655 (p90) REVERT: B 359 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7461 (tpt90) REVERT: B 781 LEU cc_start: 0.8771 (tt) cc_final: 0.8472 (mp) REVERT: B 787 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5106 (tp) REVERT: C 145 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7161 (mmt180) REVERT: C 388 PHE cc_start: 0.7518 (m-80) cc_final: 0.7067 (m-80) REVERT: C 518 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: C 674 ASP cc_start: 0.7535 (m-30) cc_final: 0.6782 (p0) REVERT: C 759 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: D 107 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6934 (t80) REVERT: D 280 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8273 (t80) REVERT: D 356 TYR cc_start: 0.4781 (p90) cc_final: 0.4497 (p90) REVERT: D 387 PHE cc_start: 0.7348 (t80) cc_final: 0.7144 (t80) REVERT: D 433 GLU cc_start: 0.8200 (mp0) cc_final: 0.7972 (mp0) REVERT: D 549 GLN cc_start: 0.7349 (mt0) cc_final: 0.6792 (pp30) REVERT: D 601 TRP cc_start: 0.7559 (t-100) cc_final: 0.7273 (t-100) REVERT: D 755 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6511 (t80) REVERT: E 69 ASP cc_start: 0.7720 (m-30) cc_final: 0.7493 (m-30) REVERT: E 194 GLN cc_start: 0.6389 (tm130) cc_final: 0.5787 (mp10) REVERT: H 32 PHE cc_start: 0.3179 (OUTLIER) cc_final: 0.2859 (m-80) outliers start: 88 outliers final: 29 residues processed: 497 average time/residue: 0.2211 time to fit residues: 179.6090 Evaluate side-chains 421 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 383 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 755 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 287 optimal weight: 0.0270 chunk 309 optimal weight: 4.9990 chunk 372 optimal weight: 30.0000 chunk 417 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 328 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 overall best weight: 2.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 698 GLN B 491 GLN C 483 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.221975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172630 restraints weight = 50857.984| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.99 r_work: 0.3657 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36397 Z= 0.221 Angle : 0.613 11.521 49033 Z= 0.321 Chirality : 0.043 0.175 5235 Planarity : 0.004 0.061 6216 Dihedral : 7.247 85.729 4881 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.62 % Allowed : 24.94 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4155 helix: 0.65 (0.10), residues: 2476 sheet: -0.88 (0.34), residues: 216 loop : -1.05 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 380 TYR 0.024 0.002 TYR A 166 PHE 0.019 0.002 PHE B 699 TRP 0.024 0.002 TRP D 448 HIS 0.008 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00522 (36397) covalent geometry : angle 0.61276 (49033) hydrogen bonds : bond 0.04076 ( 1758) hydrogen bonds : angle 4.83438 ( 5076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 412 time to evaluate : 0.870 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: A 378 TYR cc_start: 0.7376 (t80) cc_final: 0.7150 (t80) REVERT: A 414 TYR cc_start: 0.8102 (t80) cc_final: 0.7881 (t80) REVERT: A 588 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8537 (tp) REVERT: B 134 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6578 (p90) REVERT: B 287 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7446 (m) REVERT: B 293 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 357 MET cc_start: 0.8245 (tpt) cc_final: 0.7963 (mmt) REVERT: B 448 TRP cc_start: 0.8824 (m-10) cc_final: 0.8419 (m-10) REVERT: B 502 ARG cc_start: 0.6451 (ptm160) cc_final: 0.6011 (ptp90) REVERT: B 610 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: B 626 GLU cc_start: 0.8601 (tp30) cc_final: 0.8393 (mt-10) REVERT: B 781 LEU cc_start: 0.8826 (tt) cc_final: 0.8459 (mp) REVERT: B 787 ILE cc_start: 0.5406 (OUTLIER) cc_final: 0.4573 (tp) REVERT: B 810 HIS cc_start: 0.8278 (t-90) cc_final: 0.8034 (t-170) REVERT: B 862 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7198 (mt) REVERT: C 101 ASP cc_start: 0.7765 (m-30) cc_final: 0.7482 (m-30) REVERT: C 372 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.3160 (tptt) REVERT: C 388 PHE cc_start: 0.7488 (m-80) cc_final: 0.7221 (m-80) REVERT: C 447 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7619 (tpm170) REVERT: C 674 ASP cc_start: 0.7532 (m-30) cc_final: 0.6562 (p0) REVERT: C 748 ASP cc_start: 0.4907 (OUTLIER) cc_final: 0.3996 (m-30) REVERT: D 107 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7017 (t80) REVERT: D 280 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8359 (t80) REVERT: D 433 GLU cc_start: 0.8194 (mp0) cc_final: 0.7970 (mp0) REVERT: D 511 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5789 (m-80) REVERT: E 62 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7568 (p) REVERT: E 194 GLN cc_start: 0.6425 (tm130) cc_final: 0.5907 (mp10) REVERT: H 32 PHE cc_start: 0.2891 (OUTLIER) cc_final: 0.2389 (m-80) outliers start: 141 outliers final: 59 residues processed: 520 average time/residue: 0.1956 time to fit residues: 168.6036 Evaluate side-chains 457 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 384 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 356 TYR Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 226 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 405 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 365 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN B 475 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.223313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.174867 restraints weight = 50895.623| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.01 r_work: 0.3689 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36397 Z= 0.138 Angle : 0.549 12.192 49033 Z= 0.287 Chirality : 0.040 0.171 5235 Planarity : 0.003 0.052 6216 Dihedral : 6.795 77.935 4881 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.85 % Allowed : 25.86 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.13), residues: 4155 helix: 0.78 (0.10), residues: 2467 sheet: -0.83 (0.34), residues: 216 loop : -1.01 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.020 0.001 TYR B 755 PHE 0.026 0.001 PHE E 67 TRP 0.018 0.001 TRP E 72 HIS 0.009 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00320 (36397) covalent geometry : angle 0.54875 (49033) hydrogen bonds : bond 0.03612 ( 1758) hydrogen bonds : angle 4.65471 ( 5076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 417 time to evaluate : 1.360 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: A 378 TYR cc_start: 0.7359 (t80) cc_final: 0.7089 (t80) REVERT: A 414 TYR cc_start: 0.8006 (t80) cc_final: 0.7771 (t80) REVERT: A 588 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 698 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: B 134 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6802 (p90) REVERT: B 357 MET cc_start: 0.8173 (tpt) cc_final: 0.7880 (mmt) REVERT: B 531 MET cc_start: 0.8977 (mmp) cc_final: 0.8618 (mmt) REVERT: B 781 LEU cc_start: 0.8747 (tt) cc_final: 0.8448 (mp) REVERT: B 862 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7146 (mt) REVERT: B 930 MET cc_start: 0.6833 (mmt) cc_final: 0.5117 (ptt) REVERT: C 101 ASP cc_start: 0.7758 (m-30) cc_final: 0.7415 (m-30) REVERT: C 388 PHE cc_start: 0.7645 (m-80) cc_final: 0.7311 (m-80) REVERT: C 674 ASP cc_start: 0.7627 (m-30) cc_final: 0.6637 (p0) REVERT: C 759 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: D 107 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7056 (t80) REVERT: D 280 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (t80) REVERT: D 433 GLU cc_start: 0.8244 (mp0) cc_final: 0.8008 (mp0) REVERT: D 511 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: E 21 LEU cc_start: 0.7581 (pt) cc_final: 0.6990 (tt) REVERT: E 194 GLN cc_start: 0.6498 (tm130) cc_final: 0.5941 (mp10) REVERT: E 210 ASN cc_start: 0.7791 (p0) cc_final: 0.7318 (m-40) REVERT: H 32 PHE cc_start: 0.2745 (OUTLIER) cc_final: 0.2183 (m-80) outliers start: 111 outliers final: 52 residues processed: 496 average time/residue: 0.1999 time to fit residues: 165.8060 Evaluate side-chains 443 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 82 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 406 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN B 125 ASN B 609 HIS B 765 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 109 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.222953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164182 restraints weight = 51047.183| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.62 r_work: 0.3625 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36397 Z= 0.148 Angle : 0.553 12.492 49033 Z= 0.288 Chirality : 0.040 0.168 5235 Planarity : 0.003 0.050 6216 Dihedral : 6.588 70.854 4881 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 25.45 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4155 helix: 0.85 (0.10), residues: 2464 sheet: -0.69 (0.36), residues: 206 loop : -1.02 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.024 0.001 TYR B 755 PHE 0.021 0.001 PHE E 68 TRP 0.021 0.002 TRP E 72 HIS 0.009 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00347 (36397) covalent geometry : angle 0.55261 (49033) hydrogen bonds : bond 0.03551 ( 1758) hydrogen bonds : angle 4.58554 ( 5076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 415 time to evaluate : 1.409 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: A 588 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 698 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: B 293 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 357 MET cc_start: 0.8167 (tpt) cc_final: 0.7815 (mmt) REVERT: B 781 LEU cc_start: 0.8711 (tt) cc_final: 0.8444 (mp) REVERT: B 862 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7056 (mt) REVERT: B 930 MET cc_start: 0.6766 (mmt) cc_final: 0.5048 (ptt) REVERT: C 101 ASP cc_start: 0.7684 (m-30) cc_final: 0.7395 (m-30) REVERT: C 388 PHE cc_start: 0.7675 (m-80) cc_final: 0.7295 (m-80) REVERT: C 748 ASP cc_start: 0.5368 (OUTLIER) cc_final: 0.4729 (m-30) REVERT: C 759 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6831 (pt0) REVERT: D 107 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6949 (t80) REVERT: D 144 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: D 280 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8405 (t80) REVERT: D 511 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: D 610 GLN cc_start: 0.7824 (tp40) cc_final: 0.7135 (tp40) REVERT: E 21 LEU cc_start: 0.7598 (pt) cc_final: 0.7068 (tt) REVERT: E 194 GLN cc_start: 0.6484 (tm130) cc_final: 0.5965 (mp10) REVERT: E 210 ASN cc_start: 0.7768 (p0) cc_final: 0.7262 (m-40) REVERT: H 32 PHE cc_start: 0.2556 (OUTLIER) cc_final: 0.2002 (m-80) outliers start: 117 outliers final: 67 residues processed: 501 average time/residue: 0.2094 time to fit residues: 176.0442 Evaluate side-chains 465 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 176 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 378 optimal weight: 0.0270 chunk 321 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 355 optimal weight: 0.0000 chunk 308 optimal weight: 0.0270 overall best weight: 0.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN B 523 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.225122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.177180 restraints weight = 51095.665| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.23 r_work: 0.3710 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 36397 Z= 0.109 Angle : 0.529 13.368 49033 Z= 0.277 Chirality : 0.039 0.213 5235 Planarity : 0.003 0.053 6216 Dihedral : 6.264 63.379 4879 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.52 % Allowed : 25.86 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4155 helix: 0.96 (0.11), residues: 2467 sheet: -0.64 (0.36), residues: 206 loop : -0.96 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 285 TYR 0.026 0.001 TYR A 223 PHE 0.030 0.001 PHE C 381 TRP 0.017 0.001 TRP C 143 HIS 0.022 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00238 (36397) covalent geometry : angle 0.52904 (49033) hydrogen bonds : bond 0.03318 ( 1758) hydrogen bonds : angle 4.45268 ( 5076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 431 time to evaluate : 1.173 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: A 698 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6829 (mt0) REVERT: A 744 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8533 (t80) REVERT: B 357 MET cc_start: 0.8028 (tpt) cc_final: 0.7791 (mmt) REVERT: B 781 LEU cc_start: 0.8679 (tt) cc_final: 0.8397 (mp) REVERT: B 862 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7110 (mt) REVERT: C 388 PHE cc_start: 0.7441 (m-80) cc_final: 0.7112 (m-80) REVERT: C 611 TYR cc_start: 0.7815 (t80) cc_final: 0.7449 (t80) REVERT: C 759 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: D 107 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6863 (t80) REVERT: D 144 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7819 (mtmm) REVERT: D 280 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.8146 (t80) REVERT: D 482 TYR cc_start: 0.6804 (t80) cc_final: 0.6604 (t80) REVERT: D 610 GLN cc_start: 0.7827 (tp40) cc_final: 0.7399 (tp40) REVERT: D 877 PHE cc_start: 0.0997 (OUTLIER) cc_final: -0.0304 (m-80) REVERT: E 21 LEU cc_start: 0.7520 (pt) cc_final: 0.6890 (tt) REVERT: E 194 GLN cc_start: 0.6456 (tm130) cc_final: 0.6000 (mp10) REVERT: E 210 ASN cc_start: 0.7589 (p0) cc_final: 0.7114 (m-40) REVERT: F 208 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8095 (pp) REVERT: F 223 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6887 (mt) REVERT: H 32 PHE cc_start: 0.2655 (OUTLIER) cc_final: 0.1992 (m-80) outliers start: 98 outliers final: 55 residues processed: 501 average time/residue: 0.2113 time to fit residues: 174.6152 Evaluate side-chains 448 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 382 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 324 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 383 optimal weight: 0.6980 chunk 319 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.222976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.172939 restraints weight = 51137.035| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.96 r_work: 0.3695 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36397 Z= 0.138 Angle : 0.556 13.271 49033 Z= 0.287 Chirality : 0.040 0.311 5235 Planarity : 0.003 0.050 6216 Dihedral : 6.139 59.812 4879 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.52 % Allowed : 25.96 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4155 helix: 0.99 (0.11), residues: 2463 sheet: -0.80 (0.35), residues: 228 loop : -0.93 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 760 TYR 0.024 0.001 TYR C 709 PHE 0.023 0.001 PHE C 381 TRP 0.025 0.002 TRP E 72 HIS 0.009 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00322 (36397) covalent geometry : angle 0.55552 (49033) hydrogen bonds : bond 0.03381 ( 1758) hydrogen bonds : angle 4.44116 ( 5076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 394 time to evaluate : 1.051 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: A 694 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 698 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: A 721 TYR cc_start: 0.8748 (t80) cc_final: 0.7966 (t80) REVERT: A 744 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (t80) REVERT: B 357 MET cc_start: 0.8279 (tpt) cc_final: 0.7974 (mmt) REVERT: B 425 ILE cc_start: 0.7651 (mm) cc_final: 0.7369 (mt) REVERT: B 448 TRP cc_start: 0.8730 (m-10) cc_final: 0.8145 (m-10) REVERT: B 495 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8272 (tp) REVERT: B 526 ASP cc_start: 0.7186 (m-30) cc_final: 0.6971 (t70) REVERT: B 781 LEU cc_start: 0.8732 (tt) cc_final: 0.8428 (mp) REVERT: B 862 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7110 (mt) REVERT: B 930 MET cc_start: 0.6745 (mmt) cc_final: 0.5138 (ptt) REVERT: C 101 ASP cc_start: 0.7643 (m-30) cc_final: 0.7142 (m-30) REVERT: C 233 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8023 (mtt-85) REVERT: C 388 PHE cc_start: 0.7612 (m-80) cc_final: 0.7242 (m-80) REVERT: C 518 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: C 748 ASP cc_start: 0.5015 (OUTLIER) cc_final: 0.4325 (m-30) REVERT: C 759 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: D 107 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7057 (t80) REVERT: D 144 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: D 280 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8350 (t80) REVERT: D 610 GLN cc_start: 0.7872 (tp40) cc_final: 0.7469 (tp40) REVERT: D 669 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6911 (ptp-110) REVERT: D 877 PHE cc_start: 0.0818 (OUTLIER) cc_final: 0.0369 (m-80) REVERT: E 194 GLN cc_start: 0.6472 (tm130) cc_final: 0.5974 (mp10) REVERT: E 210 ASN cc_start: 0.7721 (p0) cc_final: 0.7141 (m-40) REVERT: F 176 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6431 (mmm-85) REVERT: F 223 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6967 (mt) REVERT: H 32 PHE cc_start: 0.2611 (OUTLIER) cc_final: 0.2028 (m-80) REVERT: H 48 LYS cc_start: 0.4714 (OUTLIER) cc_final: 0.4464 (ttpt) outliers start: 98 outliers final: 63 residues processed: 468 average time/residue: 0.2064 time to fit residues: 161.9993 Evaluate side-chains 461 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 549 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 398 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 266 optimal weight: 40.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 990 ASN ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.220121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164137 restraints weight = 50381.704| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.02 r_work: 0.3586 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 36397 Z= 0.242 Angle : 0.626 12.187 49033 Z= 0.325 Chirality : 0.043 0.279 5235 Planarity : 0.004 0.051 6216 Dihedral : 6.170 57.165 4879 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.72 % Allowed : 25.78 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4155 helix: 0.81 (0.10), residues: 2466 sheet: -0.51 (0.38), residues: 198 loop : -1.02 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 247 TYR 0.022 0.002 TYR A 166 PHE 0.026 0.002 PHE A 699 TRP 0.020 0.002 TRP C 143 HIS 0.014 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00579 (36397) covalent geometry : angle 0.62606 (49033) hydrogen bonds : bond 0.03832 ( 1758) hydrogen bonds : angle 4.64311 ( 5076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 398 time to evaluate : 1.460 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: A 744 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 287 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7633 (m) REVERT: B 357 MET cc_start: 0.8366 (tpt) cc_final: 0.8044 (mmt) REVERT: B 425 ILE cc_start: 0.8084 (mm) cc_final: 0.7845 (mt) REVERT: B 495 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8343 (tp) REVERT: B 781 LEU cc_start: 0.8779 (tt) cc_final: 0.8473 (mp) REVERT: B 804 TYR cc_start: 0.7460 (m-80) cc_final: 0.6939 (m-80) REVERT: B 862 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7250 (mt) REVERT: B 930 MET cc_start: 0.6698 (mmt) cc_final: 0.5032 (ptt) REVERT: C 101 ASP cc_start: 0.7754 (m-30) cc_final: 0.7286 (m-30) REVERT: C 233 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8066 (mtt-85) REVERT: C 388 PHE cc_start: 0.7643 (m-80) cc_final: 0.7254 (m-80) REVERT: C 518 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: C 759 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: D 107 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7189 (t80) REVERT: D 134 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: D 280 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8386 (t80) REVERT: D 424 PHE cc_start: 0.7350 (t80) cc_final: 0.7002 (t80) REVERT: D 537 LYS cc_start: 0.8739 (tttm) cc_final: 0.8505 (tppt) REVERT: D 541 ILE cc_start: 0.8864 (pt) cc_final: 0.8634 (tt) REVERT: D 610 GLN cc_start: 0.7927 (tp40) cc_final: 0.7523 (tp40) REVERT: D 669 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6901 (ptp-110) REVERT: D 687 TYR cc_start: 0.8294 (t80) cc_final: 0.7913 (t80) REVERT: D 866 MET cc_start: 0.0658 (OUTLIER) cc_final: 0.0338 (mmt) REVERT: D 877 PHE cc_start: 0.0715 (OUTLIER) cc_final: -0.0509 (m-80) REVERT: D 1001 MET cc_start: 0.1847 (tpp) cc_final: 0.1599 (tpp) REVERT: E 194 GLN cc_start: 0.6617 (tm130) cc_final: 0.6124 (mp10) REVERT: F 176 ARG cc_start: 0.6897 (mmm-85) cc_final: 0.6615 (mmm-85) REVERT: H 48 LYS cc_start: 0.4611 (OUTLIER) cc_final: 0.4274 (tmmt) outliers start: 106 outliers final: 72 residues processed: 478 average time/residue: 0.1989 time to fit residues: 158.9896 Evaluate side-chains 460 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 375 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 866 MET Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 122 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 352 optimal weight: 6.9990 chunk 390 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 332 HIS A 990 ASN B 377 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.221451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.167527 restraints weight = 50461.214| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.18 r_work: 0.3635 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36397 Z= 0.180 Angle : 0.598 12.474 49033 Z= 0.310 Chirality : 0.042 0.266 5235 Planarity : 0.003 0.048 6216 Dihedral : 6.061 56.640 4879 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.54 % Allowed : 26.27 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4155 helix: 0.83 (0.10), residues: 2471 sheet: -0.75 (0.36), residues: 220 loop : -0.97 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 348 TYR 0.028 0.001 TYR C 709 PHE 0.022 0.002 PHE C 559 TRP 0.020 0.002 TRP A 919 HIS 0.021 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00428 (36397) covalent geometry : angle 0.59786 (49033) hydrogen bonds : bond 0.03576 ( 1758) hydrogen bonds : angle 4.58210 ( 5076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 401 time to evaluate : 1.407 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: A 744 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: B 287 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7602 (m) REVERT: B 357 MET cc_start: 0.8284 (tpt) cc_final: 0.8041 (mmt) REVERT: B 425 ILE cc_start: 0.8010 (mm) cc_final: 0.7774 (mt) REVERT: B 448 TRP cc_start: 0.8856 (m-10) cc_final: 0.8268 (m-10) REVERT: B 781 LEU cc_start: 0.8740 (tt) cc_final: 0.8425 (mp) REVERT: B 804 TYR cc_start: 0.7444 (m-80) cc_final: 0.6942 (m-80) REVERT: B 862 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7053 (mt) REVERT: C 101 ASP cc_start: 0.7607 (m-30) cc_final: 0.7088 (m-30) REVERT: C 233 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8140 (mtt-85) REVERT: C 388 PHE cc_start: 0.7659 (m-80) cc_final: 0.7268 (m-80) REVERT: C 518 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: C 531 MET cc_start: 0.9289 (mmt) cc_final: 0.8986 (mmt) REVERT: C 759 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: D 107 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 134 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: D 280 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8378 (t80) REVERT: D 421 MET cc_start: 0.7381 (mtt) cc_final: 0.6446 (mmm) REVERT: D 424 PHE cc_start: 0.7282 (t80) cc_final: 0.6935 (t80) REVERT: D 537 LYS cc_start: 0.8748 (tttm) cc_final: 0.8489 (tppt) REVERT: D 541 ILE cc_start: 0.8888 (pt) cc_final: 0.8659 (tt) REVERT: D 610 GLN cc_start: 0.7910 (tp40) cc_final: 0.7502 (tp40) REVERT: D 633 GLU cc_start: -0.0168 (OUTLIER) cc_final: -0.1027 (tp30) REVERT: D 669 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6846 (ptp-110) REVERT: D 687 TYR cc_start: 0.8366 (t80) cc_final: 0.7996 (t80) REVERT: D 704 MET cc_start: 0.4758 (pmm) cc_final: 0.4416 (mtm) REVERT: D 877 PHE cc_start: 0.0743 (OUTLIER) cc_final: -0.0502 (m-80) REVERT: D 1001 MET cc_start: 0.1879 (tpp) cc_final: 0.1625 (tpp) REVERT: E 194 GLN cc_start: 0.6589 (tm130) cc_final: 0.6093 (mp10) REVERT: F 223 LEU cc_start: 0.7304 (mt) cc_final: 0.6699 (mt) REVERT: G 208 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.5734 (tp) REVERT: H 48 LYS cc_start: 0.4603 (OUTLIER) cc_final: 0.4336 (ttpt) outliers start: 99 outliers final: 69 residues processed: 478 average time/residue: 0.2041 time to fit residues: 162.3545 Evaluate side-chains 461 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 379 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 44 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 366 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 323 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.216413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153324 restraints weight = 51138.844| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.54 r_work: 0.3552 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36397 Z= 0.129 Angle : 0.570 12.378 49033 Z= 0.295 Chirality : 0.040 0.264 5235 Planarity : 0.003 0.056 6216 Dihedral : 5.913 59.089 4879 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.11 % Allowed : 26.68 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4155 helix: 0.93 (0.11), residues: 2466 sheet: -0.72 (0.37), residues: 220 loop : -0.93 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 760 TYR 0.027 0.001 TYR C 709 PHE 0.026 0.001 PHE E 67 TRP 0.018 0.001 TRP D 601 HIS 0.011 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00298 (36397) covalent geometry : angle 0.57041 (49033) hydrogen bonds : bond 0.03369 ( 1758) hydrogen bonds : angle 4.47410 ( 5076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 404 time to evaluate : 1.368 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: A 414 TYR cc_start: 0.8101 (t80) cc_final: 0.7883 (t80) REVERT: A 744 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: A 755 TYR cc_start: 0.8805 (t80) cc_final: 0.8586 (t80) REVERT: B 270 ASP cc_start: 0.8232 (t70) cc_final: 0.7956 (t0) REVERT: B 287 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7657 (m) REVERT: B 357 MET cc_start: 0.8375 (tpt) cc_final: 0.8163 (mmt) REVERT: B 425 ILE cc_start: 0.7952 (mm) cc_final: 0.7699 (mt) REVERT: B 448 TRP cc_start: 0.8858 (m-10) cc_final: 0.8243 (m-10) REVERT: B 755 TYR cc_start: 0.8887 (t80) cc_final: 0.8594 (t80) REVERT: B 763 LYS cc_start: 0.8101 (tppt) cc_final: 0.7712 (mmtp) REVERT: B 781 LEU cc_start: 0.8688 (tt) cc_final: 0.8370 (mp) REVERT: B 804 TYR cc_start: 0.7291 (m-80) cc_final: 0.6851 (m-80) REVERT: B 862 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7107 (mt) REVERT: C 101 ASP cc_start: 0.7848 (m-30) cc_final: 0.7293 (m-30) REVERT: C 233 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8174 (mtt-85) REVERT: C 388 PHE cc_start: 0.7649 (m-80) cc_final: 0.7288 (m-80) REVERT: C 518 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: C 531 MET cc_start: 0.9272 (mmt) cc_final: 0.8959 (mmt) REVERT: C 611 TYR cc_start: 0.7948 (t80) cc_final: 0.7559 (t80) REVERT: C 759 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6969 (pt0) REVERT: D 107 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7203 (t80) REVERT: D 134 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: D 144 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7982 (mtmm) REVERT: D 280 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8458 (t80) REVERT: D 421 MET cc_start: 0.7172 (mtt) cc_final: 0.6272 (mmm) REVERT: D 537 LYS cc_start: 0.8738 (tttm) cc_final: 0.8477 (tppt) REVERT: D 541 ILE cc_start: 0.8849 (pt) cc_final: 0.8637 (tt) REVERT: D 610 GLN cc_start: 0.7932 (tp40) cc_final: 0.7697 (tp40) REVERT: D 633 GLU cc_start: -0.0293 (OUTLIER) cc_final: -0.1040 (tp30) REVERT: D 669 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6601 (ptp-110) REVERT: D 877 PHE cc_start: 0.0792 (OUTLIER) cc_final: -0.0445 (m-80) REVERT: D 1001 MET cc_start: 0.1809 (tpp) cc_final: 0.1592 (tpp) REVERT: E 194 GLN cc_start: 0.6690 (tm130) cc_final: 0.6200 (mp10) REVERT: G 208 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5733 (tp) REVERT: H 48 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.4271 (tmmt) outliers start: 82 outliers final: 60 residues processed: 464 average time/residue: 0.2235 time to fit residues: 171.4245 Evaluate side-chains 457 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 383 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 270 optimal weight: 6.9990 chunk 377 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 372 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.216579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150244 restraints weight = 51112.519| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.85 r_work: 0.3549 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.263 36397 Z= 0.169 Angle : 0.670 59.199 49033 Z= 0.365 Chirality : 0.042 0.746 5235 Planarity : 0.003 0.053 6216 Dihedral : 5.918 59.082 4879 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 2.00 % Allowed : 26.84 % Favored : 71.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4155 helix: 0.93 (0.11), residues: 2467 sheet: -0.71 (0.37), residues: 220 loop : -0.93 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 760 TYR 0.023 0.001 TYR C 709 PHE 0.020 0.001 PHE C 559 TRP 0.017 0.002 TRP E 72 HIS 0.009 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00384 (36397) covalent geometry : angle 0.66983 (49033) hydrogen bonds : bond 0.03386 ( 1758) hydrogen bonds : angle 4.47874 ( 5076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11420.73 seconds wall clock time: 195 minutes 51.82 seconds (11751.82 seconds total)