Starting phenix.real_space_refine on Mon Aug 25 17:35:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfn_37497/08_2025/8wfn_37497.map" } resolution = 4.48 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= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 19101 2.51 5 N 4763 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 8016 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 944} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 8117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 8117 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 956} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 851 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5585 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 652} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5492 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 646} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 5 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 5.40, per 1000 atoms: 0.18 Number of scatterers: 29532 At special positions: 0 Unit cell: (105.4, 132.6, 243.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5557 8.00 N 4763 7.00 C 19101 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: 2.13 Conformation dependent library (CDL) restraints added in 761.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 14 sheets defined 66.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.587A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.735A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.696A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.661A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.050A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.791A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.591A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.517A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.780A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.722A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.671A pdb=" N PHE A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.529A pdb=" N SER A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 466 removed outlier: 3.689A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 493 Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.857A 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 525 through 531 removed outlier: 4.598A pdb=" N ASN A 529 " --> 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 546 removed outlier: 3.701A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.741A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.774A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.901A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 648 through 658 removed outlier: 4.160A pdb=" N HIS A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.629A pdb=" N SER A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.626A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.868A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 841 through 845 removed outlier: 4.056A pdb=" N LEU A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 900 Processing helix chain 'A' and resid 911 through 922 removed outlier: 3.707A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.739A pdb=" N GLU A 931 " --> pdb=" O ASN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.538A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 removed outlier: 4.146A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.759A pdb=" N LYS A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.668A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.654A pdb=" N THR B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.612A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.688A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.064A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.701A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 4.648A pdb=" N ASP B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.197A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.989A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 302' Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.966A pdb=" N LYS B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 467 through 494 removed outlier: 4.443A pdb=" N TYR B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.045A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.957A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 4.048A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.245A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.686A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.748A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.592A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.705A pdb=" N HIS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.795A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.062A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.967A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.024A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 4.010A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 833 through 841 Processing helix chain 'B' and resid 848 through 857 removed outlier: 3.759A pdb=" N HIS B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 878 through 900 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.543A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 3.941A pdb=" N LEU B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 removed outlier: 3.626A pdb=" N GLY B 972 " --> pdb=" O GLY B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 991 removed outlier: 4.280A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 4.003A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.660A pdb=" N LEU D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.553A pdb=" N THR E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.515A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 removed outlier: 3.740A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 115 through 125 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.810A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.796A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.702A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.749A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 295 removed outlier: 4.204A pdb=" N ASP E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.779A pdb=" N LYS E 331 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 376 through 392 Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 448 through 457 removed outlier: 4.852A pdb=" N TYR E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 456 " --> pdb=" O TYR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 491 removed outlier: 3.808A pdb=" N ILE E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN E 483 " --> pdb=" O TYR E 479 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 486 " --> pdb=" O TYR E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.991A pdb=" N THR E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 545 removed outlier: 3.555A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 572 Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.078A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.771A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 626 Processing helix chain 'E' and resid 648 through 658 Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 680 through 689 removed outlier: 3.510A pdb=" N ILE E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 698 Processing helix chain 'E' and resid 707 through 724 Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'E' and resid 750 through 764 Processing helix chain 'E' and resid 768 through 777 removed outlier: 3.581A pdb=" N ILE E 772 " --> pdb=" O PRO E 768 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 774 " --> pdb=" O SER E 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 40 Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.608A pdb=" N THR G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 Processing helix chain 'G' and resid 81 through 94 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 96 through 108 removed outlier: 4.386A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 removed outlier: 4.055A pdb=" N LYS G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.736A pdb=" N ALA G 161 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.538A pdb=" N TYR G 197 " --> pdb=" O TYR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 316 through 322 removed outlier: 4.264A pdb=" N ALA G 321 " --> pdb=" O PRO G 318 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 322 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 333 removed outlier: 3.706A pdb=" N LYS G 331 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS G 332 " --> pdb=" O ASP G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 366 Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 374 through 391 Processing helix chain 'G' and resid 411 through 416 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 433 through 445 Processing helix chain 'G' and resid 447 through 462 Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 467 through 494 removed outlier: 4.245A pdb=" N TYR G 471 " --> pdb=" O ASN G 467 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 494 " --> pdb=" O THR G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 519 Processing helix chain 'G' and resid 525 through 531 removed outlier: 4.004A pdb=" N ASN G 529 " --> pdb=" O ASP G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 539 Processing helix chain 'G' and resid 540 through 544 Processing helix chain 'G' and resid 551 through 552 No H-bonds generated for 'chain 'G' and resid 551 through 552' Processing helix chain 'G' and resid 554 through 554 No H-bonds generated for 'chain 'G' and resid 554 through 554' Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 580 through 596 Processing helix chain 'G' and resid 600 through 604 removed outlier: 4.038A pdb=" N VAL G 603 " --> pdb=" O LEU G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 628 removed outlier: 3.738A pdb=" N ALA G 623 " --> pdb=" O LEU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 658 removed outlier: 4.159A pdb=" N HIS G 658 " --> pdb=" O ASN G 654 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 671 removed outlier: 3.593A pdb=" N ILE G 664 " --> pdb=" O LYS G 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 701 removed outlier: 3.834A pdb=" N ALA G 701 " --> pdb=" O LYS G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 723 removed outlier: 4.286A pdb=" N GLN G 711 " --> pdb=" O VAL G 707 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 713 " --> pdb=" O TYR G 709 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 714 " --> pdb=" O THR G 710 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 716 " --> pdb=" O PHE G 712 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 718 " --> pdb=" O SER G 714 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 723 " --> pdb=" O ALA G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 743 Processing helix chain 'G' and resid 750 through 765 Processing helix chain 'G' and resid 770 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.070A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 130 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 197 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 171 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 11 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 24 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 13 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.290A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 244 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 6.453A 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 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 21 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG D 15 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR D 171 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 197 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.527A pdb=" N PHE E 244 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 574 through 575 removed outlier: 3.716A pdb=" N TYR E 574 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA F 30 " --> pdb=" O TYR E 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 150 through 152 removed outlier: 5.976A pdb=" N SER G 150 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS G 169 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 152 " --> pdb=" O LYS G 169 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 129 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS G 128 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 213 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE G 246 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE G 215 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 68 removed outlier: 4.320A pdb=" N PHE F 67 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 24 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR F 171 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN F 197 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 192 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 233 " --> pdb=" O GLN F 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 26 1578 hydrogen bonds defined for protein. 4536 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: 5.53 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9078 1.34 - 1.46: 5564 1.46 - 1.57: 15333 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 30159 Sorted by residual: bond pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " ideal model delta sigma weight residual 1.534 1.547 -0.012 6.80e-03 2.16e+04 3.24e+00 bond pdb=" C ILE G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.02e+00 bond pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.97e+00 bond pdb=" C ILE B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.10e+00 bond pdb=" C ASP E 281 " pdb=" N TYR E 282 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.27e-02 6.20e+03 1.84e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 40019 2.29 - 4.58: 492 4.58 - 6.87: 54 6.87 - 9.16: 21 9.16 - 11.45: 4 Bond angle restraints: 40590 Sorted by residual: angle pdb=" C ARG G 86 " pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 120.24 125.76 -5.52 6.30e-01 2.52e+00 7.68e+01 angle pdb=" C PRO B 74 " pdb=" N LYS B 75 " pdb=" CA LYS B 75 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ARG E 247 " pdb=" N THR E 248 " pdb=" CA THR E 248 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C MET G 124 " pdb=" N ASN G 125 " pdb=" CA ASN G 125 " ideal model delta sigma weight residual 121.80 132.22 -10.42 2.44e+00 1.68e-01 1.82e+01 angle pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " pdb=" CG TYR B 282 " ideal model delta sigma weight residual 113.90 121.40 -7.50 1.80e+00 3.09e-01 1.73e+01 ... (remaining 40585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15884 17.22 - 34.43: 1536 34.43 - 51.65: 416 51.65 - 68.86: 99 68.86 - 86.08: 10 Dihedral angle restraints: 17945 sinusoidal: 7369 harmonic: 10576 Sorted by residual: dihedral pdb=" CA PHE B 921 " pdb=" C PHE B 921 " pdb=" N LEU B 922 " pdb=" CA LEU B 922 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA SER B 287 " pdb=" C SER B 287 " pdb=" N ALA B 288 " pdb=" CA ALA B 288 " ideal model delta harmonic sigma weight residual 180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PHE E 550 " pdb=" C PHE E 550 " pdb=" N LEU E 551 " pdb=" CA LEU E 551 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2940 0.043 - 0.086: 1106 0.086 - 0.129: 247 0.129 - 0.171: 56 0.171 - 0.214: 2 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CB THR E 562 " pdb=" CA THR E 562 " pdb=" OG1 THR E 562 " pdb=" CG2 THR E 562 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR E 248 " pdb=" N THR E 248 " pdb=" C THR E 248 " pdb=" CB THR E 248 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE G 275 " pdb=" CA ILE G 275 " pdb=" CG1 ILE G 275 " pdb=" CG2 ILE G 275 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 4348 not shown) Planarity restraints: 5159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 317 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO B 318 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 317 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO E 318 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 318 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 318 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 115 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO G 116 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 116 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 116 " 0.034 5.00e-02 4.00e+02 ... (remaining 5156 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4497 2.76 - 3.30: 29167 3.30 - 3.83: 52789 3.83 - 4.37: 60079 4.37 - 4.90: 96199 Nonbonded interactions: 242731 Sorted by model distance: nonbonded pdb=" OH TYR E 436 " pdb=" O VAL E 470 " model vdw 2.228 3.040 nonbonded pdb=" O GLU B 516 " pdb=" OG1 THR B 520 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR E 472 " pdb=" O LEU E 542 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR E 218 " pdb=" O ASP E 222 " model vdw 2.269 3.040 nonbonded pdb=" O VAL G 707 " pdb=" OG1 THR G 710 " model vdw 2.269 3.040 ... (remaining 242726 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 546 or resid 548 through 638 or resid 642 throu \ gh 830 or resid 832 through 843 or resid 847 through 1005)) selection = (chain 'B' and (resid 23 through 73 or resid 81 through 110 or (resid 111 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thro \ ugh 160 or resid 165 through 269 or resid 279 through 801 or (resid 802 and (nam \ e N or name CA or name C or name O or name CB )) or resid 803 through 1005)) } ncs_group { reference = (chain 'C' and (resid 5 through 33 or resid 52 through 177 or resid 190 through \ 236)) selection = (chain 'D' and (resid 5 through 209 or resid 217 through 227 or (resid 228 throu \ gh 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thr \ ough 235 or (resid 236 and (name N or name CA or name C or name O or name CB ))) \ ) } ncs_group { reference = (chain 'E' and (resid 22 through 179 or resid 186 through 217 or resid 222 throu \ gh 297 or resid 316 through 396 or resid 409 through 426 or resid 432 through 49 \ 8 or resid 502 or resid 507 through 553 or resid 555 through 573 or resid 580 th \ rough 627 or resid 649 through 672 or resid 682 through 727 or resid 730 through \ 766 or resid 769 through 777)) selection = (chain 'G' and (resid 22 through 71 or resid 80 through 110 or resid 112 through \ 125 or resid 130 through 145 or resid 165 through 343 or resid 347 through 353 \ or resid 355 through 372 or resid 375 through 498 or resid 517 or resid 522 or r \ esid 527 through 627 or resid 649 through 689 or resid 691 through 700 or resid \ 706 through 777)) } 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 group one per residue 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: 0.770 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.570 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30159 Z= 0.176 Angle : 0.700 11.453 40590 Z= 0.395 Chirality : 0.046 0.214 4351 Planarity : 0.005 0.076 5159 Dihedral : 14.999 86.081 11109 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 5.17 % Allowed : 12.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.12), residues: 3455 helix: -1.17 (0.10), residues: 2022 sheet: -0.37 (0.37), residues: 218 loop : -1.60 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 247 TYR 0.018 0.002 TYR D 175 PHE 0.022 0.002 PHE A 559 TRP 0.013 0.001 TRP G 601 HIS 0.008 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00342 (30159) covalent geometry : angle 0.70007 (40590) hydrogen bonds : bond 0.15583 ( 1564) hydrogen bonds : angle 6.65224 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 468 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: A 204 MET cc_start: 0.9637 (tmm) cc_final: 0.9191 (tmm) REVERT: A 226 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8663 (p0) REVERT: A 260 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: A 290 MET cc_start: 0.9604 (ttt) cc_final: 0.9347 (ttt) REVERT: A 421 MET cc_start: 0.9381 (ppp) cc_final: 0.9059 (ppp) REVERT: A 504 TYR cc_start: 0.7366 (t80) cc_final: 0.6997 (t80) REVERT: A 519 MET cc_start: 0.9134 (mmp) cc_final: 0.8387 (mmm) REVERT: A 524 ILE cc_start: 0.9515 (pt) cc_final: 0.8855 (mp) REVERT: A 527 LEU cc_start: 0.9509 (mt) cc_final: 0.9186 (mt) REVERT: A 557 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9063 (mtmm) REVERT: A 588 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9448 (tt) REVERT: A 660 LYS cc_start: 0.9377 (tptp) cc_final: 0.9052 (tptp) REVERT: A 662 ASP cc_start: 0.9146 (p0) cc_final: 0.8796 (p0) REVERT: A 693 GLU cc_start: 0.9403 (tp30) cc_final: 0.8652 (tp30) REVERT: A 704 MET cc_start: 0.7364 (ptp) cc_final: 0.6931 (ptp) REVERT: A 712 PHE cc_start: 0.9342 (t80) cc_final: 0.9009 (t80) REVERT: A 866 MET cc_start: 0.9488 (tmm) cc_final: 0.9256 (tmm) REVERT: A 913 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7931 (ppp) REVERT: A 938 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 100 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: B 105 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9105 (mmmm) REVERT: B 183 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 315 LYS cc_start: 0.9308 (tttt) cc_final: 0.9014 (tttt) REVERT: B 331 LYS cc_start: 0.9571 (pttp) cc_final: 0.9353 (mtmm) REVERT: B 361 PHE cc_start: 0.9474 (m-80) cc_final: 0.8788 (m-10) REVERT: B 396 MET cc_start: 0.9002 (mpp) cc_final: 0.8749 (mpp) REVERT: B 412 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 441 PHE cc_start: 0.9498 (m-10) cc_final: 0.9222 (m-80) REVERT: B 448 TRP cc_start: 0.9121 (m-10) cc_final: 0.8879 (m-10) REVERT: B 525 ASP cc_start: 0.9426 (p0) cc_final: 0.9124 (p0) REVERT: B 540 LYS cc_start: 0.9196 (tmmt) cc_final: 0.8979 (tmtt) REVERT: B 553 ASP cc_start: 0.9544 (p0) cc_final: 0.9320 (p0) REVERT: B 616 MET cc_start: 0.9192 (ttm) cc_final: 0.8856 (ttm) REVERT: B 618 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9216 (mm) REVERT: B 759 GLU cc_start: 0.9677 (OUTLIER) cc_final: 0.9263 (mm-30) REVERT: B 915 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9361 (p) REVERT: B 959 LEU cc_start: 0.9724 (tp) cc_final: 0.9516 (tp) REVERT: B 975 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.7406 (p90) REVERT: B 976 MET cc_start: 0.8872 (mpp) cc_final: 0.8668 (mmt) REVERT: B 994 LYS cc_start: 0.9197 (mppt) cc_final: 0.8974 (mmtm) REVERT: B 997 LEU cc_start: 0.9719 (mt) cc_final: 0.9471 (tt) REVERT: C 67 PHE cc_start: 0.8892 (m-80) cc_final: 0.8593 (m-80) REVERT: D 63 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 192 TYR cc_start: 0.8700 (m-80) cc_final: 0.8456 (m-80) REVERT: D 231 MET cc_start: 0.8201 (pmm) cc_final: 0.7856 (pmm) REVERT: E 197 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: E 202 ASN cc_start: 0.9070 (t0) cc_final: 0.8800 (t0) REVERT: E 282 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: G 91 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7744 (t80) REVERT: G 202 ASN cc_start: 0.8846 (m110) cc_final: 0.8538 (t0) REVERT: G 396 MET cc_start: 0.6287 (mtt) cc_final: 0.6047 (mmt) REVERT: G 471 TYR cc_start: 0.7109 (t80) cc_final: 0.6725 (t80) REVERT: G 587 ARG cc_start: 0.9295 (tpp80) cc_final: 0.9051 (mmp80) REVERT: G 697 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8609 (ptmm) outliers start: 166 outliers final: 28 residues processed: 606 average time/residue: 0.1620 time to fit residues: 159.1455 Evaluate side-chains 355 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 192 ASN A 263 ASN A 351 ASN A 493 ASN A 591 ASN A 606 HIS A 852 HIS ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS B 78 ASN B 109 GLN B 226 ASN B 467 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN E 332 HIS E 591 ASN ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 263 ASN G 521 ASN G 666 ASN G 765 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046148 restraints weight = 229972.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047601 restraints weight = 140099.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048624 restraints weight = 95805.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049333 restraints weight = 71100.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049794 restraints weight = 56470.336| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 30159 Z= 0.246 Angle : 0.658 8.180 40590 Z= 0.367 Chirality : 0.043 0.201 4351 Planarity : 0.005 0.057 5159 Dihedral : 5.191 23.852 3886 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % 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 aren not related in a simple way. whole: -0.90 (0.14), residues: 3455 helix: -0.06 (0.11), residues: 2106 sheet: -0.35 (0.35), residues: 220 loop : -1.49 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 587 TYR 0.030 0.002 TYR G 92 PHE 0.036 0.002 PHE G 559 TRP 0.014 0.002 TRP A 757 HIS 0.008 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00490 (30159) covalent geometry : angle 0.65755 (40590) hydrogen bonds : bond 0.04543 ( 1564) hydrogen bonds : angle 5.37054 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8918 (tpp) cc_final: 0.8302 (tpp) REVERT: A 202 ASN cc_start: 0.9484 (t0) cc_final: 0.9267 (t0) REVERT: A 204 MET cc_start: 0.9598 (tmm) cc_final: 0.9122 (tmm) REVERT: A 227 MET cc_start: 0.9112 (mmp) cc_final: 0.8902 (mmt) REVERT: A 290 MET cc_start: 0.9480 (ttt) cc_final: 0.8929 (ttm) REVERT: A 519 MET cc_start: 0.9257 (mmp) cc_final: 0.8952 (mmm) REVERT: A 524 ILE cc_start: 0.9423 (pt) cc_final: 0.9214 (pt) REVERT: A 647 MET cc_start: 0.9085 (mmp) cc_final: 0.8740 (mmm) REVERT: A 662 ASP cc_start: 0.9153 (p0) cc_final: 0.8899 (p0) REVERT: A 693 GLU cc_start: 0.9313 (tp30) cc_final: 0.8792 (tp30) REVERT: A 704 MET cc_start: 0.7119 (ptp) cc_final: 0.6706 (ptp) REVERT: A 712 PHE cc_start: 0.9266 (t80) cc_final: 0.9030 (t80) REVERT: A 866 MET cc_start: 0.9370 (tmm) cc_final: 0.8950 (tmm) REVERT: B 105 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8994 (mmmm) REVERT: B 168 LEU cc_start: 0.9672 (tp) cc_final: 0.9420 (tp) REVERT: B 315 LYS cc_start: 0.9445 (tttt) cc_final: 0.9075 (tttt) REVERT: B 361 PHE cc_start: 0.9330 (m-80) cc_final: 0.8936 (m-80) REVERT: B 434 ASP cc_start: 0.9497 (m-30) cc_final: 0.9063 (t70) REVERT: B 441 PHE cc_start: 0.9587 (m-10) cc_final: 0.9029 (m-80) REVERT: B 448 TRP cc_start: 0.8906 (m-10) cc_final: 0.8662 (m-10) REVERT: B 553 ASP cc_start: 0.9621 (p0) cc_final: 0.9263 (p0) REVERT: B 759 GLU cc_start: 0.9810 (mm-30) cc_final: 0.9585 (mm-30) REVERT: B 776 ASP cc_start: 0.9042 (t70) cc_final: 0.8678 (t0) REVERT: C 67 PHE cc_start: 0.8865 (m-80) cc_final: 0.8549 (m-80) REVERT: D 192 TYR cc_start: 0.8789 (m-80) cc_final: 0.8449 (m-80) REVERT: D 231 MET cc_start: 0.8432 (pmm) cc_final: 0.7918 (pmm) REVERT: E 202 ASN cc_start: 0.9084 (t0) cc_final: 0.8827 (t0) REVERT: E 261 TYR cc_start: 0.8551 (m-10) cc_final: 0.7875 (m-80) REVERT: E 290 MET cc_start: 0.9423 (ptt) cc_final: 0.8721 (tmm) REVERT: G 148 TYR cc_start: 0.9392 (t80) cc_final: 0.9090 (t80) REVERT: G 202 ASN cc_start: 0.8827 (m110) cc_final: 0.8533 (t0) REVERT: G 322 LEU cc_start: 0.8725 (pp) cc_final: 0.8502 (pp) REVERT: G 396 MET cc_start: 0.5918 (mtt) cc_final: 0.5705 (mmt) REVERT: G 471 TYR cc_start: 0.7971 (t80) cc_final: 0.7367 (t80) REVERT: G 587 ARG cc_start: 0.9530 (tpp80) cc_final: 0.9098 (mmp80) REVERT: G 594 PHE cc_start: 0.9724 (t80) cc_final: 0.9372 (t80) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.1744 time to fit residues: 102.9638 Evaluate side-chains 256 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 132 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 292 optimal weight: 0.0670 chunk 149 optimal weight: 0.9980 chunk 341 optimal weight: 10.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS A 939 GLN A 975 HIS B 477 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 HIS E 609 HIS ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 467 ASN G 782 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048014 restraints weight = 215546.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049531 restraints weight = 132716.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050583 restraints weight = 91457.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051333 restraints weight = 68073.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051839 restraints weight = 53850.849| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30159 Z= 0.112 Angle : 0.534 9.608 40590 Z= 0.286 Chirality : 0.041 0.158 4351 Planarity : 0.004 0.066 5159 Dihedral : 4.815 23.288 3886 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 aren not related in a simple way. whole: -0.43 (0.14), residues: 3455 helix: 0.38 (0.11), residues: 2098 sheet: -0.11 (0.36), residues: 208 loop : -1.45 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.026 0.001 TYR E 721 PHE 0.021 0.001 PHE D 195 TRP 0.010 0.001 TRP B 143 HIS 0.016 0.001 HIS B 810 Details of bonding type rmsd covalent geometry : bond 0.00237 (30159) covalent geometry : angle 0.53399 (40590) hydrogen bonds : bond 0.03748 ( 1564) hydrogen bonds : angle 4.87546 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8856 (tpp) cc_final: 0.7784 (tpp) REVERT: A 202 ASN cc_start: 0.9373 (t0) cc_final: 0.9148 (t0) REVERT: A 204 MET cc_start: 0.9617 (tmm) cc_final: 0.9313 (tmm) REVERT: A 227 MET cc_start: 0.9176 (mmp) cc_final: 0.8906 (mmt) REVERT: A 290 MET cc_start: 0.9515 (ttt) cc_final: 0.8968 (ttm) REVERT: A 519 MET cc_start: 0.9223 (mmp) cc_final: 0.8858 (mmm) REVERT: A 524 ILE cc_start: 0.9381 (pt) cc_final: 0.8645 (mm) REVERT: A 527 LEU cc_start: 0.9522 (mt) cc_final: 0.9311 (mt) REVERT: A 543 GLU cc_start: 0.9475 (pm20) cc_final: 0.9240 (pm20) REVERT: A 550 PHE cc_start: 0.9475 (t80) cc_final: 0.9233 (t80) REVERT: A 578 MET cc_start: 0.8984 (ppp) cc_final: 0.8672 (ppp) REVERT: A 647 MET cc_start: 0.8928 (mmp) cc_final: 0.8631 (mmm) REVERT: A 693 GLU cc_start: 0.9285 (tp30) cc_final: 0.8702 (tp30) REVERT: A 704 MET cc_start: 0.6837 (ptp) cc_final: 0.6526 (ptp) REVERT: A 712 PHE cc_start: 0.9247 (t80) cc_final: 0.9005 (t80) REVERT: A 866 MET cc_start: 0.9339 (tmm) cc_final: 0.8834 (tmm) REVERT: B 315 LYS cc_start: 0.9485 (tttt) cc_final: 0.9114 (tttt) REVERT: B 361 PHE cc_start: 0.9248 (m-80) cc_final: 0.8658 (m-80) REVERT: B 375 LYS cc_start: 0.8747 (mmpt) cc_final: 0.8300 (mmmt) REVERT: B 434 ASP cc_start: 0.9482 (m-30) cc_final: 0.8944 (t70) REVERT: B 441 PHE cc_start: 0.9573 (m-10) cc_final: 0.8963 (m-80) REVERT: B 448 TRP cc_start: 0.8937 (m-10) cc_final: 0.8729 (m-10) REVERT: B 521 ASN cc_start: 0.8895 (m-40) cc_final: 0.8673 (m-40) REVERT: B 553 ASP cc_start: 0.9550 (p0) cc_final: 0.9134 (p0) REVERT: B 759 GLU cc_start: 0.9822 (mm-30) cc_final: 0.9563 (mm-30) REVERT: B 776 ASP cc_start: 0.9067 (t70) cc_final: 0.8654 (t0) REVERT: C 67 PHE cc_start: 0.8807 (m-80) cc_final: 0.8572 (m-80) REVERT: C 195 PHE cc_start: 0.9284 (m-80) cc_final: 0.8744 (m-80) REVERT: C 219 LYS cc_start: 0.9039 (tptp) cc_final: 0.8722 (tptp) REVERT: C 231 MET cc_start: 0.7943 (mmm) cc_final: 0.7742 (mmm) REVERT: D 231 MET cc_start: 0.8581 (pmm) cc_final: 0.8106 (pmm) REVERT: E 202 ASN cc_start: 0.9062 (t0) cc_final: 0.8822 (t0) REVERT: E 261 TYR cc_start: 0.8429 (m-10) cc_final: 0.7964 (m-80) REVERT: E 290 MET cc_start: 0.9446 (ptt) cc_final: 0.8755 (tmm) REVERT: E 340 PHE cc_start: 0.8318 (m-10) cc_final: 0.8113 (m-10) REVERT: G 148 TYR cc_start: 0.9452 (t80) cc_final: 0.9158 (t80) REVERT: G 202 ASN cc_start: 0.8754 (m110) cc_final: 0.8435 (t0) REVERT: G 227 MET cc_start: 0.9333 (tmm) cc_final: 0.9105 (tmm) REVERT: G 471 TYR cc_start: 0.7953 (t80) cc_final: 0.7366 (t80) REVERT: G 587 ARG cc_start: 0.9508 (tpp80) cc_final: 0.9048 (mmp-170) REVERT: G 594 PHE cc_start: 0.9603 (t80) cc_final: 0.9177 (t80) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1647 time to fit residues: 102.6492 Evaluate side-chains 264 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 105 optimal weight: 0.0870 chunk 263 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 303 optimal weight: 0.0570 chunk 339 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 312 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS A 910 ASN B 109 GLN B 786 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN E 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.063344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047628 restraints weight = 220804.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049123 restraints weight = 135374.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.050187 restraints weight = 93038.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050935 restraints weight = 69100.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051432 restraints weight = 54456.237| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30159 Z= 0.120 Angle : 0.525 9.224 40590 Z= 0.282 Chirality : 0.040 0.163 4351 Planarity : 0.004 0.073 5159 Dihedral : 4.598 23.966 3886 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % 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 aren not related in a simple way. whole: -0.14 (0.14), residues: 3455 helix: 0.63 (0.11), residues: 2104 sheet: -0.06 (0.36), residues: 209 loop : -1.37 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 165 TYR 0.019 0.001 TYR E 721 PHE 0.026 0.001 PHE E 100 TRP 0.021 0.001 TRP E 448 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00251 (30159) covalent geometry : angle 0.52527 (40590) hydrogen bonds : bond 0.03493 ( 1564) hydrogen bonds : angle 4.68038 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8836 (tpp) cc_final: 0.7733 (tpp) REVERT: A 202 ASN cc_start: 0.9371 (t0) cc_final: 0.9143 (t0) REVERT: A 204 MET cc_start: 0.9626 (tmm) cc_final: 0.9317 (tmm) REVERT: A 227 MET cc_start: 0.9141 (mmp) cc_final: 0.8859 (mmt) REVERT: A 290 MET cc_start: 0.9533 (ttt) cc_final: 0.8991 (ttm) REVERT: A 519 MET cc_start: 0.9196 (mmp) cc_final: 0.8871 (mmm) REVERT: A 524 ILE cc_start: 0.9368 (pt) cc_final: 0.9140 (pt) REVERT: A 550 PHE cc_start: 0.9459 (t80) cc_final: 0.9255 (t80) REVERT: A 587 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8267 (ptm-80) REVERT: A 693 GLU cc_start: 0.9214 (tp30) cc_final: 0.8606 (tp30) REVERT: A 704 MET cc_start: 0.6878 (ptp) cc_final: 0.6557 (ptp) REVERT: A 712 PHE cc_start: 0.9254 (t80) cc_final: 0.9023 (t80) REVERT: A 866 MET cc_start: 0.9334 (tmm) cc_final: 0.8867 (tmm) REVERT: B 204 MET cc_start: 0.9508 (tpt) cc_final: 0.9089 (tmm) REVERT: B 290 MET cc_start: 0.9316 (ptm) cc_final: 0.9097 (ppp) REVERT: B 315 LYS cc_start: 0.9476 (tttt) cc_final: 0.9137 (tttt) REVERT: B 361 PHE cc_start: 0.9217 (m-80) cc_final: 0.8608 (m-80) REVERT: B 375 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8286 (mmmt) REVERT: B 434 ASP cc_start: 0.9467 (m-30) cc_final: 0.8956 (t70) REVERT: B 441 PHE cc_start: 0.9552 (m-10) cc_final: 0.8975 (m-80) REVERT: B 448 TRP cc_start: 0.8780 (m-10) cc_final: 0.8545 (m-10) REVERT: B 521 ASN cc_start: 0.8982 (m-40) cc_final: 0.8711 (m-40) REVERT: B 553 ASP cc_start: 0.9528 (p0) cc_final: 0.9095 (p0) REVERT: B 595 LEU cc_start: 0.9425 (mt) cc_final: 0.9187 (mt) REVERT: B 759 GLU cc_start: 0.9803 (mm-30) cc_final: 0.9597 (mm-30) REVERT: B 776 ASP cc_start: 0.9039 (t70) cc_final: 0.8568 (t0) REVERT: C 195 PHE cc_start: 0.9269 (m-80) cc_final: 0.8809 (m-80) REVERT: D 231 MET cc_start: 0.8556 (pmm) cc_final: 0.8080 (pmm) REVERT: E 202 ASN cc_start: 0.8865 (t0) cc_final: 0.8500 (t0) REVERT: E 261 TYR cc_start: 0.8601 (m-10) cc_final: 0.8019 (m-80) REVERT: E 340 PHE cc_start: 0.8359 (m-10) cc_final: 0.8140 (m-10) REVERT: G 148 TYR cc_start: 0.9444 (t80) cc_final: 0.9134 (t80) REVERT: G 202 ASN cc_start: 0.8705 (m110) cc_final: 0.8351 (t0) REVERT: G 227 MET cc_start: 0.9331 (tmm) cc_final: 0.9094 (tmm) REVERT: G 357 MET cc_start: 0.9343 (mmm) cc_final: 0.9085 (mmm) REVERT: G 471 TYR cc_start: 0.7669 (t80) cc_final: 0.7038 (t80) REVERT: G 587 ARG cc_start: 0.9495 (tpp80) cc_final: 0.9092 (mmp-170) REVERT: G 594 PHE cc_start: 0.9609 (t80) cc_final: 0.9193 (t80) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1675 time to fit residues: 99.7201 Evaluate side-chains 268 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 299 optimal weight: 0.5980 chunk 291 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 63 optimal weight: 0.0030 chunk 231 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN E 339 HIS E 349 HIS E 493 ASN G 67 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.063663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047749 restraints weight = 214840.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049271 restraints weight = 132966.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.050335 restraints weight = 91562.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051077 restraints weight = 68181.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051634 restraints weight = 53821.542| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30159 Z= 0.108 Angle : 0.517 9.059 40590 Z= 0.275 Chirality : 0.040 0.204 4351 Planarity : 0.003 0.069 5159 Dihedral : 4.458 24.111 3886 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3455 helix: 0.80 (0.11), residues: 2114 sheet: -0.09 (0.36), residues: 207 loop : -1.32 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.020 0.001 TYR A 260 PHE 0.032 0.001 PHE G 91 TRP 0.016 0.001 TRP G 757 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00226 (30159) covalent geometry : angle 0.51651 (40590) hydrogen bonds : bond 0.03329 ( 1564) hydrogen bonds : angle 4.55311 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8818 (tpp) cc_final: 0.8179 (tpp) REVERT: A 204 MET cc_start: 0.9632 (tmm) cc_final: 0.9338 (tmm) REVERT: A 227 MET cc_start: 0.9140 (mmp) cc_final: 0.8938 (mmm) REVERT: A 290 MET cc_start: 0.9539 (ttt) cc_final: 0.9296 (ttm) REVERT: A 519 MET cc_start: 0.9275 (mmp) cc_final: 0.9059 (mmm) REVERT: A 578 MET cc_start: 0.9092 (ppp) cc_final: 0.8667 (ppp) REVERT: A 647 MET cc_start: 0.8939 (mmp) cc_final: 0.8644 (mmm) REVERT: A 693 GLU cc_start: 0.9256 (tp30) cc_final: 0.8611 (tp30) REVERT: A 704 MET cc_start: 0.6839 (ptp) cc_final: 0.6529 (ptp) REVERT: A 712 PHE cc_start: 0.9273 (t80) cc_final: 0.9038 (t80) REVERT: A 866 MET cc_start: 0.9363 (tmm) cc_final: 0.8875 (tmm) REVERT: B 307 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9199 (mt-10) REVERT: B 315 LYS cc_start: 0.9486 (tttt) cc_final: 0.9207 (tttt) REVERT: B 361 PHE cc_start: 0.9227 (m-80) cc_final: 0.8646 (m-80) REVERT: B 375 LYS cc_start: 0.8818 (mmpt) cc_final: 0.8341 (mmmt) REVERT: B 434 ASP cc_start: 0.9509 (m-30) cc_final: 0.8901 (t70) REVERT: B 441 PHE cc_start: 0.9583 (m-10) cc_final: 0.8992 (m-80) REVERT: B 448 TRP cc_start: 0.8798 (m-10) cc_final: 0.8580 (m-10) REVERT: B 553 ASP cc_start: 0.9582 (p0) cc_final: 0.9203 (p0) REVERT: B 595 LEU cc_start: 0.9461 (mt) cc_final: 0.9214 (mt) REVERT: B 776 ASP cc_start: 0.9047 (t70) cc_final: 0.8613 (t0) REVERT: C 192 TYR cc_start: 0.8955 (m-80) cc_final: 0.8704 (m-80) REVERT: C 195 PHE cc_start: 0.9294 (m-80) cc_final: 0.8845 (m-80) REVERT: D 231 MET cc_start: 0.8576 (pmm) cc_final: 0.8033 (pmm) REVERT: E 197 TYR cc_start: 0.9101 (m-10) cc_final: 0.8671 (m-80) REVERT: E 202 ASN cc_start: 0.8880 (t0) cc_final: 0.8496 (t0) REVERT: E 261 TYR cc_start: 0.8576 (m-10) cc_final: 0.8000 (m-80) REVERT: E 290 MET cc_start: 0.9473 (ptt) cc_final: 0.9002 (ppp) REVERT: E 616 MET cc_start: 0.8191 (tpt) cc_final: 0.7694 (ptm) REVERT: E 691 ILE cc_start: 0.8482 (mm) cc_final: 0.8247 (pt) REVERT: G 148 TYR cc_start: 0.9508 (t80) cc_final: 0.9195 (t80) REVERT: G 202 ASN cc_start: 0.8784 (m110) cc_final: 0.8493 (t0) REVERT: G 227 MET cc_start: 0.9330 (tmm) cc_final: 0.9076 (tmm) REVERT: G 357 MET cc_start: 0.9339 (mmm) cc_final: 0.9113 (mmm) REVERT: G 471 TYR cc_start: 0.7594 (t80) cc_final: 0.7065 (t80) REVERT: G 587 ARG cc_start: 0.9478 (tpp80) cc_final: 0.9079 (mmp80) REVERT: G 594 PHE cc_start: 0.9601 (t80) cc_final: 0.9196 (t80) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1888 time to fit residues: 113.8035 Evaluate side-chains 267 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 55 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047810 restraints weight = 221457.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049275 restraints weight = 135397.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050306 restraints weight = 92796.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050988 restraints weight = 69023.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051519 restraints weight = 54809.771| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30159 Z= 0.119 Angle : 0.518 8.777 40590 Z= 0.278 Chirality : 0.040 0.188 4351 Planarity : 0.003 0.069 5159 Dihedral : 4.401 23.813 3886 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 aren not related in a simple way. whole: 0.16 (0.14), residues: 3455 helix: 0.89 (0.11), residues: 2117 sheet: -0.08 (0.37), residues: 207 loop : -1.27 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 587 TYR 0.028 0.001 TYR B 755 PHE 0.025 0.001 PHE G 91 TRP 0.016 0.001 TRP G 757 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00249 (30159) covalent geometry : angle 0.51779 (40590) hydrogen bonds : bond 0.03297 ( 1564) hydrogen bonds : angle 4.53032 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8823 (tpp) cc_final: 0.8138 (tpp) REVERT: A 202 ASN cc_start: 0.9314 (t0) cc_final: 0.9114 (t0) REVERT: A 204 MET cc_start: 0.9632 (tmm) cc_final: 0.9354 (tmm) REVERT: A 227 MET cc_start: 0.9136 (mmp) cc_final: 0.8883 (mmm) REVERT: A 290 MET cc_start: 0.9518 (ttt) cc_final: 0.8980 (ttm) REVERT: A 519 MET cc_start: 0.9236 (mmp) cc_final: 0.8906 (mmm) REVERT: A 647 MET cc_start: 0.8846 (mmp) cc_final: 0.8639 (mmm) REVERT: A 693 GLU cc_start: 0.9186 (tp30) cc_final: 0.8551 (tp30) REVERT: A 704 MET cc_start: 0.6840 (ptp) cc_final: 0.6558 (ptp) REVERT: A 712 PHE cc_start: 0.9207 (t80) cc_final: 0.8990 (t80) REVERT: A 866 MET cc_start: 0.9336 (tmm) cc_final: 0.8847 (tmm) REVERT: B 168 LEU cc_start: 0.9552 (tp) cc_final: 0.9285 (tp) REVERT: B 307 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9178 (mt-10) REVERT: B 315 LYS cc_start: 0.9420 (tttt) cc_final: 0.9169 (tttt) REVERT: B 361 PHE cc_start: 0.9191 (m-80) cc_final: 0.8630 (m-80) REVERT: B 375 LYS cc_start: 0.8707 (mmpt) cc_final: 0.8408 (mmmt) REVERT: B 412 LEU cc_start: 0.9516 (mm) cc_final: 0.9039 (tp) REVERT: B 434 ASP cc_start: 0.9464 (m-30) cc_final: 0.8929 (t70) REVERT: B 441 PHE cc_start: 0.9552 (m-10) cc_final: 0.8962 (m-80) REVERT: B 448 TRP cc_start: 0.8766 (m-10) cc_final: 0.8560 (m-10) REVERT: B 543 GLU cc_start: 0.9420 (pm20) cc_final: 0.9214 (pm20) REVERT: B 553 ASP cc_start: 0.9522 (p0) cc_final: 0.9130 (p0) REVERT: B 776 ASP cc_start: 0.9026 (t70) cc_final: 0.8536 (t0) REVERT: C 192 TYR cc_start: 0.8880 (m-80) cc_final: 0.8573 (m-10) REVERT: D 231 MET cc_start: 0.8502 (pmm) cc_final: 0.7985 (pmm) REVERT: E 202 ASN cc_start: 0.8840 (t0) cc_final: 0.8442 (t0) REVERT: E 261 TYR cc_start: 0.8588 (m-10) cc_final: 0.8000 (m-80) REVERT: E 290 MET cc_start: 0.9468 (ptt) cc_final: 0.8985 (ppp) REVERT: E 691 ILE cc_start: 0.8573 (mm) cc_final: 0.8340 (pt) REVERT: G 148 TYR cc_start: 0.9497 (t80) cc_final: 0.9181 (t80) REVERT: G 202 ASN cc_start: 0.8660 (m110) cc_final: 0.8333 (t0) REVERT: G 227 MET cc_start: 0.9335 (tmm) cc_final: 0.9082 (tmm) REVERT: G 236 GLN cc_start: 0.8148 (tt0) cc_final: 0.7809 (tt0) REVERT: G 357 MET cc_start: 0.9358 (mmm) cc_final: 0.9135 (mmm) REVERT: G 471 TYR cc_start: 0.7661 (t80) cc_final: 0.7071 (t80) REVERT: G 587 ARG cc_start: 0.9397 (tpp80) cc_final: 0.9035 (tpp-160) REVERT: G 594 PHE cc_start: 0.9602 (t80) cc_final: 0.9211 (t80) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1925 time to fit residues: 112.1964 Evaluate side-chains 264 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 97 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 0.3980 chunk 280 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.047037 restraints weight = 227378.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048479 restraints weight = 139105.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049485 restraints weight = 95679.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.050199 restraints weight = 71124.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050658 restraints weight = 56184.204| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30159 Z= 0.151 Angle : 0.543 8.438 40590 Z= 0.294 Chirality : 0.041 0.182 4351 Planarity : 0.004 0.066 5159 Dihedral : 4.476 23.898 3886 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 aren not related in a simple way. whole: 0.12 (0.14), residues: 3455 helix: 0.85 (0.11), residues: 2118 sheet: -0.12 (0.37), residues: 207 loop : -1.26 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 566 TYR 0.019 0.001 TYR B 755 PHE 0.019 0.001 PHE G 91 TRP 0.017 0.002 TRP E 601 HIS 0.007 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00308 (30159) covalent geometry : angle 0.54258 (40590) hydrogen bonds : bond 0.03399 ( 1564) hydrogen bonds : angle 4.60878 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8701 (tpp) cc_final: 0.7924 (tpp) REVERT: A 204 MET cc_start: 0.9644 (tmm) cc_final: 0.9370 (tmm) REVERT: A 227 MET cc_start: 0.9228 (mmp) cc_final: 0.8939 (mmm) REVERT: A 290 MET cc_start: 0.9520 (ttt) cc_final: 0.8985 (ttm) REVERT: A 519 MET cc_start: 0.9178 (mmp) cc_final: 0.8848 (mmm) REVERT: A 578 MET cc_start: 0.9024 (ppp) cc_final: 0.8593 (ppp) REVERT: A 647 MET cc_start: 0.9050 (mmp) cc_final: 0.8800 (mmm) REVERT: A 693 GLU cc_start: 0.9235 (tp30) cc_final: 0.8635 (tp30) REVERT: A 704 MET cc_start: 0.7098 (ptp) cc_final: 0.6807 (ptp) REVERT: A 866 MET cc_start: 0.9361 (tmm) cc_final: 0.8897 (tmm) REVERT: B 315 LYS cc_start: 0.9437 (tttt) cc_final: 0.9190 (tttt) REVERT: B 361 PHE cc_start: 0.9211 (m-80) cc_final: 0.8650 (m-80) REVERT: B 375 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8404 (mmmt) REVERT: B 412 LEU cc_start: 0.9464 (mm) cc_final: 0.8912 (tp) REVERT: B 434 ASP cc_start: 0.9478 (m-30) cc_final: 0.8929 (t70) REVERT: B 441 PHE cc_start: 0.9562 (m-10) cc_final: 0.8990 (m-80) REVERT: B 448 TRP cc_start: 0.8852 (m-10) cc_final: 0.8587 (m-10) REVERT: B 553 ASP cc_start: 0.9542 (p0) cc_final: 0.9160 (p0) REVERT: B 595 LEU cc_start: 0.9462 (mt) cc_final: 0.9237 (mt) REVERT: B 647 MET cc_start: 0.7765 (ppp) cc_final: 0.6283 (ppp) REVERT: B 776 ASP cc_start: 0.9036 (t70) cc_final: 0.8525 (t0) REVERT: B 786 HIS cc_start: 0.8168 (t-90) cc_final: 0.7342 (t-170) REVERT: C 192 TYR cc_start: 0.8914 (m-80) cc_final: 0.8610 (m-10) REVERT: D 204 PHE cc_start: 0.7590 (t80) cc_final: 0.7389 (t80) REVERT: D 231 MET cc_start: 0.8452 (pmm) cc_final: 0.7838 (pmm) REVERT: E 202 ASN cc_start: 0.8878 (t0) cc_final: 0.8243 (t0) REVERT: E 261 TYR cc_start: 0.8738 (m-10) cc_final: 0.8181 (m-80) REVERT: E 340 PHE cc_start: 0.8421 (m-10) cc_final: 0.8182 (m-10) REVERT: E 357 MET cc_start: 0.9126 (tpt) cc_final: 0.8690 (ttt) REVERT: G 148 TYR cc_start: 0.9433 (t80) cc_final: 0.9124 (t80) REVERT: G 202 ASN cc_start: 0.8675 (m110) cc_final: 0.8389 (t0) REVERT: G 236 GLN cc_start: 0.8134 (tt0) cc_final: 0.7795 (tt0) REVERT: G 357 MET cc_start: 0.9371 (mmm) cc_final: 0.9131 (mmm) REVERT: G 471 TYR cc_start: 0.7721 (t80) cc_final: 0.7118 (t80) REVERT: G 594 PHE cc_start: 0.9607 (t80) cc_final: 0.9233 (t80) REVERT: H 206 MET cc_start: 0.3701 (tmm) cc_final: 0.3489 (tmm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1855 time to fit residues: 105.1789 Evaluate side-chains 263 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 310 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 269 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 overall best weight: 5.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** G 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 782 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.059494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044719 restraints weight = 232598.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.046019 restraints weight = 145188.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.046928 restraints weight = 101523.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047589 restraints weight = 76324.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.048034 restraints weight = 60958.283| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30159 Z= 0.251 Angle : 0.680 9.708 40590 Z= 0.374 Chirality : 0.044 0.196 4351 Planarity : 0.005 0.068 5159 Dihedral : 5.031 26.135 3886 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 aren not related in a simple way. whole: -0.49 (0.14), residues: 3455 helix: 0.33 (0.11), residues: 2102 sheet: -0.23 (0.36), residues: 209 loop : -1.45 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 987 TYR 0.025 0.002 TYR G 92 PHE 0.028 0.002 PHE E 659 TRP 0.024 0.003 TRP E 601 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00499 (30159) covalent geometry : angle 0.68024 (40590) hydrogen bonds : bond 0.04108 ( 1564) hydrogen bonds : angle 5.10577 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.9098 (t-100) cc_final: 0.8663 (t-100) REVERT: A 124 MET cc_start: 0.8908 (tpp) cc_final: 0.8687 (tpp) REVERT: A 204 MET cc_start: 0.9611 (tmm) cc_final: 0.9319 (tmm) REVERT: A 290 MET cc_start: 0.9510 (ttt) cc_final: 0.9301 (ttt) REVERT: A 647 MET cc_start: 0.9242 (mmp) cc_final: 0.8989 (mmm) REVERT: A 693 GLU cc_start: 0.9223 (tp30) cc_final: 0.8609 (tp30) REVERT: A 704 MET cc_start: 0.7618 (ptp) cc_final: 0.7395 (ptp) REVERT: A 712 PHE cc_start: 0.9354 (t80) cc_final: 0.9145 (t80) REVERT: A 866 MET cc_start: 0.9435 (tmm) cc_final: 0.8985 (tmm) REVERT: A 936 MET cc_start: 0.5637 (tpp) cc_final: 0.5394 (tpt) REVERT: B 59 TRP cc_start: 0.9161 (t-100) cc_final: 0.8915 (t-100) REVERT: B 168 LEU cc_start: 0.9567 (tp) cc_final: 0.9245 (tp) REVERT: B 315 LYS cc_start: 0.9444 (tttt) cc_final: 0.9121 (tttt) REVERT: B 361 PHE cc_start: 0.9221 (m-80) cc_final: 0.8744 (m-80) REVERT: B 434 ASP cc_start: 0.9503 (m-30) cc_final: 0.8904 (t70) REVERT: B 441 PHE cc_start: 0.9566 (m-10) cc_final: 0.9003 (m-80) REVERT: B 521 ASN cc_start: 0.9016 (m-40) cc_final: 0.8792 (m-40) REVERT: B 553 ASP cc_start: 0.9591 (p0) cc_final: 0.9278 (p0) REVERT: B 647 MET cc_start: 0.7887 (ppp) cc_final: 0.6413 (ppp) REVERT: B 688 LEU cc_start: 0.9777 (mt) cc_final: 0.9557 (mt) REVERT: B 776 ASP cc_start: 0.9171 (t70) cc_final: 0.8679 (t0) REVERT: B 786 HIS cc_start: 0.8318 (t-90) cc_final: 0.7592 (t-170) REVERT: C 192 TYR cc_start: 0.9068 (m-80) cc_final: 0.8832 (m-80) REVERT: D 231 MET cc_start: 0.8400 (pmm) cc_final: 0.7763 (pmm) REVERT: E 261 TYR cc_start: 0.9107 (m-10) cc_final: 0.8463 (m-80) REVERT: E 340 PHE cc_start: 0.8434 (m-10) cc_final: 0.8225 (m-10) REVERT: E 357 MET cc_start: 0.9140 (tpt) cc_final: 0.8689 (ttt) REVERT: E 691 ILE cc_start: 0.8769 (pt) cc_final: 0.8553 (mm) REVERT: G 148 TYR cc_start: 0.9368 (t80) cc_final: 0.9044 (t80) REVERT: G 357 MET cc_start: 0.9451 (mmm) cc_final: 0.9227 (mmm) REVERT: G 471 TYR cc_start: 0.7822 (t80) cc_final: 0.7162 (t80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1636 time to fit residues: 86.8841 Evaluate side-chains 236 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 HIS ** G 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 = 0.3443 r_free = 0.3443 target = 0.062196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046499 restraints weight = 217134.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047962 restraints weight = 133808.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048965 restraints weight = 92219.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049685 restraints weight = 68796.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050178 restraints weight = 54425.898| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30159 Z= 0.118 Angle : 0.559 9.076 40590 Z= 0.298 Chirality : 0.042 0.168 4351 Planarity : 0.003 0.064 5159 Dihedral : 4.671 24.999 3886 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 aren not related in a simple way. whole: -0.02 (0.14), residues: 3455 helix: 0.72 (0.11), residues: 2109 sheet: -0.17 (0.37), residues: 207 loop : -1.28 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 587 TYR 0.024 0.001 TYR B 721 PHE 0.019 0.001 PHE G 559 TRP 0.017 0.001 TRP G 60 HIS 0.005 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00251 (30159) covalent geometry : angle 0.55915 (40590) hydrogen bonds : bond 0.03422 ( 1564) hydrogen bonds : angle 4.67318 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.9072 (t-100) cc_final: 0.8681 (t-100) REVERT: A 204 MET cc_start: 0.9638 (tmm) cc_final: 0.9366 (tmm) REVERT: A 290 MET cc_start: 0.9562 (ttt) cc_final: 0.9223 (ttt) REVERT: A 421 MET cc_start: 0.9043 (ppp) cc_final: 0.8839 (ppp) REVERT: A 578 MET cc_start: 0.9089 (ppp) cc_final: 0.8656 (ppp) REVERT: A 647 MET cc_start: 0.9096 (mmp) cc_final: 0.8832 (mmm) REVERT: A 693 GLU cc_start: 0.9203 (tp30) cc_final: 0.8573 (tp30) REVERT: A 704 MET cc_start: 0.7850 (ptp) cc_final: 0.7635 (ptp) REVERT: A 712 PHE cc_start: 0.9321 (t80) cc_final: 0.9048 (t80) REVERT: A 866 MET cc_start: 0.9372 (tmm) cc_final: 0.8878 (tmm) REVERT: A 913 MET cc_start: 0.8150 (ppp) cc_final: 0.7903 (ppp) REVERT: B 168 LEU cc_start: 0.9528 (tp) cc_final: 0.9057 (tp) REVERT: B 204 MET cc_start: 0.9488 (tpt) cc_final: 0.9260 (tpt) REVERT: B 307 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9087 (mt-10) REVERT: B 361 PHE cc_start: 0.9234 (m-80) cc_final: 0.8862 (m-10) REVERT: B 434 ASP cc_start: 0.9488 (m-30) cc_final: 0.8852 (t70) REVERT: B 441 PHE cc_start: 0.9569 (m-10) cc_final: 0.9011 (m-80) REVERT: B 448 TRP cc_start: 0.8803 (m-10) cc_final: 0.8592 (m-10) REVERT: B 531 MET cc_start: 0.8975 (tpp) cc_final: 0.8757 (tmm) REVERT: B 540 LYS cc_start: 0.9321 (pptt) cc_final: 0.9117 (tppt) REVERT: B 553 ASP cc_start: 0.9408 (p0) cc_final: 0.9127 (p0) REVERT: B 647 MET cc_start: 0.7618 (ppp) cc_final: 0.6113 (ppp) REVERT: B 776 ASP cc_start: 0.9140 (t70) cc_final: 0.8684 (t0) REVERT: B 786 HIS cc_start: 0.8318 (t-90) cc_final: 0.7479 (t-170) REVERT: C 192 TYR cc_start: 0.8937 (m-80) cc_final: 0.8672 (m-10) REVERT: D 231 MET cc_start: 0.8382 (pmm) cc_final: 0.8040 (pmm) REVERT: E 202 ASN cc_start: 0.8996 (t0) cc_final: 0.8566 (t0) REVERT: E 261 TYR cc_start: 0.8779 (m-10) cc_final: 0.8191 (m-80) REVERT: E 290 MET cc_start: 0.9402 (ptt) cc_final: 0.8966 (ppp) REVERT: E 340 PHE cc_start: 0.8488 (m-10) cc_final: 0.8250 (m-10) REVERT: E 357 MET cc_start: 0.9107 (tpt) cc_final: 0.8663 (ttt) REVERT: E 691 ILE cc_start: 0.8701 (pt) cc_final: 0.8469 (mm) REVERT: G 148 TYR cc_start: 0.9446 (t80) cc_final: 0.9174 (t80) REVERT: G 202 ASN cc_start: 0.8769 (m-40) cc_final: 0.8530 (t0) REVERT: G 227 MET cc_start: 0.9325 (tmm) cc_final: 0.9075 (tmm) REVERT: G 357 MET cc_start: 0.9417 (mmm) cc_final: 0.9177 (mmm) REVERT: G 471 TYR cc_start: 0.7731 (t80) cc_final: 0.7099 (t80) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1827 time to fit residues: 101.8562 Evaluate side-chains 253 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 124 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS B 610 GLN B 614 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 HIS ** G 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 = 0.3435 r_free = 0.3435 target = 0.061867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046284 restraints weight = 218288.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047701 restraints weight = 134802.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048709 restraints weight = 93236.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049375 restraints weight = 69813.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.049912 restraints weight = 55768.276| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30159 Z= 0.128 Angle : 0.557 8.624 40590 Z= 0.298 Chirality : 0.042 0.225 4351 Planarity : 0.004 0.063 5159 Dihedral : 4.573 23.850 3886 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: 0.08 (0.14), residues: 3455 helix: 0.77 (0.11), residues: 2109 sheet: -0.02 (0.38), residues: 198 loop : -1.19 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 587 TYR 0.023 0.001 TYR B 721 PHE 0.019 0.001 PHE E 240 TRP 0.015 0.001 TRP A 59 HIS 0.013 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00269 (30159) covalent geometry : angle 0.55696 (40590) hydrogen bonds : bond 0.03364 ( 1564) hydrogen bonds : angle 4.64621 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.9058 (t-100) cc_final: 0.8677 (t-100) REVERT: A 124 MET cc_start: 0.8648 (tpp) cc_final: 0.8324 (tpp) REVERT: A 204 MET cc_start: 0.9652 (tmm) cc_final: 0.9382 (tmm) REVERT: A 290 MET cc_start: 0.9515 (ttt) cc_final: 0.9155 (ttt) REVERT: A 531 MET cc_start: 0.9047 (tpt) cc_final: 0.8654 (tpp) REVERT: A 578 MET cc_start: 0.9188 (ppp) cc_final: 0.8711 (ppp) REVERT: A 647 MET cc_start: 0.9112 (mmp) cc_final: 0.8836 (mmm) REVERT: A 693 GLU cc_start: 0.9198 (tp30) cc_final: 0.8556 (tp30) REVERT: A 704 MET cc_start: 0.7866 (ptp) cc_final: 0.7659 (ptp) REVERT: A 712 PHE cc_start: 0.9314 (t80) cc_final: 0.9056 (t80) REVERT: A 866 MET cc_start: 0.9358 (tmm) cc_final: 0.8891 (tmm) REVERT: B 168 LEU cc_start: 0.9521 (tp) cc_final: 0.9045 (tp) REVERT: B 204 MET cc_start: 0.9498 (tpt) cc_final: 0.9280 (tpt) REVERT: B 307 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9112 (mt-10) REVERT: B 315 LYS cc_start: 0.9497 (tttt) cc_final: 0.9176 (tttt) REVERT: B 361 PHE cc_start: 0.9368 (m-80) cc_final: 0.8985 (m-10) REVERT: B 412 LEU cc_start: 0.9355 (mm) cc_final: 0.8756 (tp) REVERT: B 434 ASP cc_start: 0.9497 (m-30) cc_final: 0.8864 (t70) REVERT: B 441 PHE cc_start: 0.9576 (m-10) cc_final: 0.9011 (m-80) REVERT: B 448 TRP cc_start: 0.8877 (m-10) cc_final: 0.8671 (m-10) REVERT: B 521 ASN cc_start: 0.9027 (m-40) cc_final: 0.8815 (m-40) REVERT: B 553 ASP cc_start: 0.9383 (p0) cc_final: 0.9133 (p0) REVERT: B 647 MET cc_start: 0.7697 (ppp) cc_final: 0.6195 (ppp) REVERT: B 776 ASP cc_start: 0.9136 (t70) cc_final: 0.8645 (t0) REVERT: B 786 HIS cc_start: 0.8385 (t-90) cc_final: 0.7748 (t70) REVERT: C 192 TYR cc_start: 0.8925 (m-80) cc_final: 0.8661 (m-10) REVERT: D 231 MET cc_start: 0.8241 (pmm) cc_final: 0.7745 (pmm) REVERT: E 202 ASN cc_start: 0.8985 (t0) cc_final: 0.8564 (t0) REVERT: E 261 TYR cc_start: 0.8774 (m-10) cc_final: 0.8177 (m-80) REVERT: E 290 MET cc_start: 0.9426 (ptt) cc_final: 0.9002 (ppp) REVERT: E 340 PHE cc_start: 0.8513 (m-10) cc_final: 0.8290 (m-10) REVERT: E 357 MET cc_start: 0.9126 (tpt) cc_final: 0.8690 (ttt) REVERT: E 616 MET cc_start: 0.8313 (tpt) cc_final: 0.7779 (ptm) REVERT: E 691 ILE cc_start: 0.8715 (pt) cc_final: 0.8475 (mm) REVERT: G 98 MET cc_start: 0.8727 (tpp) cc_final: 0.8227 (tpp) REVERT: G 148 TYR cc_start: 0.9450 (t80) cc_final: 0.9171 (t80) REVERT: G 227 MET cc_start: 0.9315 (tmm) cc_final: 0.9073 (tmm) REVERT: G 236 GLN cc_start: 0.8246 (tt0) cc_final: 0.7912 (tt0) REVERT: G 357 MET cc_start: 0.9431 (mmm) cc_final: 0.9199 (mmm) REVERT: G 471 TYR cc_start: 0.7748 (t80) cc_final: 0.7121 (t80) REVERT: G 594 PHE cc_start: 0.9581 (t80) cc_final: 0.9144 (t80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1949 time to fit residues: 107.5103 Evaluate side-chains 253 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 301 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 304 optimal weight: 0.9990 chunk 166 optimal weight: 0.2980 chunk 262 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 HIS ** G 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 ASN G 782 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.046351 restraints weight = 221204.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047774 restraints weight = 136913.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048768 restraints weight = 94806.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049496 restraints weight = 70742.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049990 restraints weight = 56033.695| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30159 Z= 0.129 Angle : 0.551 8.576 40590 Z= 0.295 Chirality : 0.041 0.167 4351 Planarity : 0.004 0.062 5159 Dihedral : 4.534 23.530 3886 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 aren not related in a simple way. whole: 0.10 (0.14), residues: 3455 helix: 0.78 (0.11), residues: 2122 sheet: 0.02 (0.38), residues: 198 loop : -1.20 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 587 TYR 0.020 0.001 TYR B 721 PHE 0.018 0.001 PHE E 240 TRP 0.015 0.001 TRP G 757 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00270 (30159) covalent geometry : angle 0.55056 (40590) hydrogen bonds : bond 0.03347 ( 1564) hydrogen bonds : angle 4.61675 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.00 seconds wall clock time: 84 minutes 27.74 seconds (5067.74 seconds total)