Starting phenix.real_space_refine on Thu Aug 6 03:13:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.map" model { file = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2026/9bha_44538.cif" } resolution = 3.5 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= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 78 5.16 5 C 8337 2.51 5 N 2246 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13264 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6251 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 769} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6245 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 769} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 215 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3} Unresolved non-hydrogen planarities: 58 Chain: "Y" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 553 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1, ' DG:plan': 5, ' DG:plan2': 5, ' DC:plan': 5, ' DC:plan2': 5, ' DT:plan': 8, ' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 209 Time building chain proxies: 2.76, per 1000 atoms: 0.21 Number of scatterers: 13264 At special positions: 0 Unit cell: (129.948, 149.94, 89.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 48 15.00 O 2555 8.00 N 2246 7.00 C 8337 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: 1.09 Conformation dependent library (CDL) restraints added in 667.7 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 60.8% alpha, 8.3% beta 1 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.922A pdb=" N GLY A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.212A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.710A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 246 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.558A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.590A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.624A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.410A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.797A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 578 through 592 removed outlier: 4.246A pdb=" N GLU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 584 " --> pdb=" O GLY A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'A' and resid 624 through 640 removed outlier: 4.123A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 677 through 688 removed outlier: 4.053A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.968A pdb=" N ALA A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 724 " --> pdb=" O PHE A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.516A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.646A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 removed outlier: 4.003A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 793 through 801 removed outlier: 4.529A pdb=" N VAL A 799 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 813 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 825 through 837 removed outlier: 4.434A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 4.252A pdb=" N GLU A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 860 " --> pdb=" O ARG A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 888 removed outlier: 4.108A pdb=" N ALA A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.732A pdb=" N GLY B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.161A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.650A pdb=" N LEU B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.518A pdb=" N VAL B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.307A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.975A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 421 through 434 Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.548A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.712A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.743A pdb=" N GLU B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 removed outlier: 4.289A pdb=" N GLU B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 640 removed outlier: 4.417A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 3.738A pdb=" N LEU B 653 " --> pdb=" O HIS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 674 removed outlier: 3.802A pdb=" N LEU B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 688 removed outlier: 4.048A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 698 removed outlier: 4.373A pdb=" N ARG B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 730 removed outlier: 3.556A pdb=" N ALA B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.531A pdb=" N GLN B 739 " --> pdb=" O ARG B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 770 removed outlier: 3.669A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 782 Processing helix chain 'B' and resid 790 through 795 removed outlier: 3.863A pdb=" N ASP B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 799 Processing helix chain 'B' and resid 803 through 815 Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 825 through 837 removed outlier: 4.222A pdb=" N VAL B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 861 removed outlier: 3.735A pdb=" N VAL B 853 " --> pdb=" O GLU B 849 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 891 removed outlier: 3.949A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 889 " --> pdb=" O MET B 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.610A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 139 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 213 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 141 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL A 215 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 143 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 260 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 312 removed outlier: 6.507A pdb=" N LEU A 309 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP A 304 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 599 Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.540A pdb=" N THR B 190 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS B 139 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL B 213 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 141 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 215 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 143 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 260 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 111 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.361A pdb=" N LEU B 309 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP B 304 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 340 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA B 442 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU B 342 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 414 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA8, first strand: chain 'B' and resid 595 through 598 645 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.47 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: 3985 1.34 - 1.45: 1839 1.45 - 1.57: 7516 1.57 - 1.69: 95 1.69 - 1.81: 124 Bond restraints: 13559 Sorted by residual: bond pdb=" C3' DA Y 40 " pdb=" C2' DA Y 40 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.60e+01 bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.57e+01 bond pdb=" C3' DA Y 35 " pdb=" C2' DA Y 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 bond pdb=" C3' DT Y 45 " pdb=" C2' DT Y 45 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.11e+00 bond pdb=" C3' DG Y 50 " pdb=" C2' DG Y 50 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.91e+00 ... (remaining 13554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 17886 1.74 - 3.49: 524 3.49 - 5.23: 46 5.23 - 6.98: 2 6.98 - 8.72: 1 Bond angle restraints: 18459 Sorted by residual: angle pdb=" O5' DA Y 35 " pdb=" C5' DA Y 35 " pdb=" C4' DA Y 35 " ideal model delta sigma weight residual 109.40 113.57 -4.17 8.00e-01 1.56e+00 2.72e+01 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 110.10 105.55 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" O5' DA Y 37 " pdb=" C5' DA Y 37 " pdb=" C4' DA Y 37 " ideal model delta sigma weight residual 109.40 112.95 -3.55 8.00e-01 1.56e+00 1.97e+01 angle pdb=" N3 DT Y 43 " pdb=" C4 DT Y 43 " pdb=" O4 DT Y 43 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT Y 39 " pdb=" C4 DT Y 39 " pdb=" O4 DT Y 39 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 18454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7386 17.80 - 35.59: 562 35.59 - 53.39: 177 53.39 - 71.19: 57 71.19 - 88.99: 16 Dihedral angle restraints: 8198 sinusoidal: 3605 harmonic: 4593 Sorted by residual: dihedral pdb=" CA HIS B 816 " pdb=" C HIS B 816 " pdb=" N THR B 817 " pdb=" CA THR B 817 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR A 662 " pdb=" C THR A 662 " pdb=" N THR A 663 " pdb=" CA THR A 663 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA LEU A 102 " pdb=" C LEU A 102 " pdb=" N GLY A 103 " pdb=" CA GLY A 103 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1438 0.040 - 0.079: 540 0.079 - 0.118: 146 0.118 - 0.158: 35 0.158 - 0.197: 4 Chirality restraints: 2163 Sorted by residual: chirality pdb=" C4' DA Y 40 " pdb=" C5' DA Y 40 " pdb=" O4' DA Y 40 " pdb=" C3' DA Y 40 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB THR B 655 " pdb=" CA THR B 655 " pdb=" OG1 THR B 655 " pdb=" CG2 THR B 655 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" C4' DT Y 39 " pdb=" C5' DT Y 39 " pdb=" O4' DT Y 39 " pdb=" C3' DT Y 39 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 2160 not shown) Planarity restraints: 2189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 39 " -0.045 2.00e-02 2.50e+03 3.27e-02 2.68e+01 pdb=" N1 DT Y 39 " 0.087 2.00e-02 2.50e+03 pdb=" C2 DT Y 39 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DT Y 39 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT Y 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT Y 39 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT Y 39 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT Y 39 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT Y 39 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT Y 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 35 " -0.036 2.00e-02 2.50e+03 2.54e-02 1.77e+01 pdb=" N9 DA Y 35 " 0.071 2.00e-02 2.50e+03 pdb=" C8 DA Y 35 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DA Y 35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA Y 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA Y 35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA Y 35 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA Y 35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA Y 35 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA Y 35 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA Y 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 22 " 0.025 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" N1 DT Y 22 " -0.061 2.00e-02 2.50e+03 pdb=" C2 DT Y 22 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DT Y 22 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT Y 22 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT Y 22 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT Y 22 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT Y 22 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT Y 22 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT Y 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 2186 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4199 2.85 - 3.37: 12597 3.37 - 3.88: 20600 3.88 - 4.39: 25175 4.39 - 4.90: 41596 Nonbonded interactions: 104167 Sorted by model distance: nonbonded pdb=" OG1 THR A 655 " pdb=" OG SER A 722 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASP B 634 " pdb=" NH2 ARG B 711 " model vdw 2.344 3.120 nonbonded pdb=" OD2 ASP A 727 " pdb=" OH TYR A 741 " model vdw 2.389 3.040 nonbonded pdb=" OH TYR B 113 " pdb=" O LYS B 121 " model vdw 2.394 3.040 nonbonded pdb=" OD1 ASN B 773 " pdb=" N MET B 774 " model vdw 2.404 3.120 ... (remaining 104162 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 67 through 566 or resid 577 through 863 or resid 870 throu \ gh 892)) selection = (chain 'B' and (resid 67 through 600 or resid 605 through 892)) } 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: 2.960 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.035 13559 Z= 0.237 Angle : 0.683 8.721 18459 Z= 0.460 Chirality : 0.046 0.197 2163 Planarity : 0.008 0.077 2189 Dihedral : 15.466 88.987 5218 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.42 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1564 helix: -2.28 (0.14), residues: 848 sheet: 0.82 (0.39), residues: 151 loop : 0.40 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG A 460 TYR 0.024 0.005 TYR A 239 PHE 0.020 0.001 PHE B 658 TRP 0.017 0.002 TRP B 666 HIS 0.007 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.24 (13559) covalent geometry : angle 0.68285 / 0.46 (18459) hydrogen bonds : bond 0.20393 / 13.26 ( 647) hydrogen bonds : angle 8.16642 / 5.75 ( 1870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7696 (p-90) cc_final: 0.7210 (p-90) REVERT: A 446 LEU cc_start: 0.6996 (mt) cc_final: 0.6755 (mt) REVERT: B 70 LEU cc_start: 0.8280 (tp) cc_final: 0.8017 (tt) REVERT: B 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6625 (m-30) REVERT: B 678 THR cc_start: 0.8179 (p) cc_final: 0.7656 (t) REVERT: B 753 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7170 (mm-40) REVERT: B 855 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6027 (mp0) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1223 time to fit residues: 54.5587 Evaluate side-chains 173 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 325 HIS A 649 HIS B 219 HIS B 284 HIS B 338 HIS B 384 GLN B 738 ASN B 780 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137371 restraints weight = 17511.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137556 restraints weight = 17301.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138635 restraints weight = 15720.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138959 restraints weight = 12609.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139388 restraints weight = 11320.378| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13559 Z= 0.159 Angle : 0.674 11.012 18459 Z= 0.360 Chirality : 0.044 0.182 2163 Planarity : 0.005 0.047 2189 Dihedral : 15.730 88.992 2185 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.90 % Allowed : 7.76 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1564 helix: -0.61 (0.16), residues: 887 sheet: 0.87 (0.38), residues: 152 loop : 0.53 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 708 TYR 0.023 0.002 TYR B 331 PHE 0.017 0.001 PHE B 415 TRP 0.017 0.002 TRP A 74 HIS 0.006 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (13559) covalent geometry : angle 0.67419 / 0.36 (18459) hydrogen bonds : bond 0.04826 / 3.22 ( 647) hydrogen bonds : angle 5.17252 / 3.63 ( 1870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8355 (tt) cc_final: 0.8078 (mm) REVERT: A 95 TRP cc_start: 0.7762 (p-90) cc_final: 0.7208 (p-90) REVERT: A 634 ASP cc_start: 0.7279 (m-30) cc_final: 0.7030 (m-30) REVERT: A 758 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: B 70 LEU cc_start: 0.8266 (tp) cc_final: 0.7758 (tt) REVERT: B 73 ASN cc_start: 0.7762 (m-40) cc_final: 0.7362 (m110) REVERT: B 126 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6438 (mp0) REVERT: B 169 ASP cc_start: 0.7087 (t0) cc_final: 0.6563 (m-30) REVERT: B 183 SER cc_start: 0.8137 (m) cc_final: 0.7803 (t) REVERT: B 678 THR cc_start: 0.7901 (p) cc_final: 0.7486 (t) outliers start: 26 outliers final: 14 residues processed: 223 average time/residue: 0.1093 time to fit residues: 35.6111 Evaluate side-chains 181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN B 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133969 restraints weight = 17988.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133422 restraints weight = 16000.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134807 restraints weight = 15138.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134921 restraints weight = 12733.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135595 restraints weight = 11309.858| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13559 Z= 0.155 Angle : 0.610 9.673 18459 Z= 0.325 Chirality : 0.042 0.168 2163 Planarity : 0.004 0.037 2189 Dihedral : 15.521 88.549 2185 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.83 % Allowed : 10.18 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1564 helix: -0.20 (0.16), residues: 895 sheet: 0.78 (0.38), residues: 164 loop : 0.55 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.012 0.001 TYR B 331 PHE 0.015 0.001 PHE A 765 TRP 0.011 0.001 TRP A 661 HIS 0.010 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (13559) covalent geometry : angle 0.60951 / 0.33 (18459) hydrogen bonds : bond 0.04530 / 3.03 ( 647) hydrogen bonds : angle 4.75132 / 3.33 ( 1870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8377 (tt) cc_final: 0.8140 (mm) REVERT: A 95 TRP cc_start: 0.7604 (p-90) cc_final: 0.7094 (p-90) REVERT: A 634 ASP cc_start: 0.7203 (m-30) cc_final: 0.6994 (m-30) REVERT: A 660 ASP cc_start: 0.6780 (m-30) cc_final: 0.6367 (t0) REVERT: B 70 LEU cc_start: 0.8247 (tp) cc_final: 0.7688 (tt) REVERT: B 73 ASN cc_start: 0.7885 (m-40) cc_final: 0.7475 (m110) REVERT: B 87 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B 126 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6575 (mp0) REVERT: B 169 ASP cc_start: 0.7094 (t0) cc_final: 0.6527 (m-30) REVERT: B 183 SER cc_start: 0.8179 (m) cc_final: 0.7781 (t) REVERT: B 587 MET cc_start: 0.7382 (ttm) cc_final: 0.7094 (mtp) outliers start: 25 outliers final: 17 residues processed: 194 average time/residue: 0.0997 time to fit residues: 29.0594 Evaluate side-chains 171 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 647 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134721 restraints weight = 17783.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135348 restraints weight = 16172.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136096 restraints weight = 15485.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136562 restraints weight = 12046.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136933 restraints weight = 10905.106| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13559 Z= 0.126 Angle : 0.584 11.209 18459 Z= 0.305 Chirality : 0.040 0.140 2163 Planarity : 0.003 0.035 2189 Dihedral : 15.402 89.444 2185 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.12 % Allowed : 10.54 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1564 helix: 0.13 (0.17), residues: 899 sheet: 0.77 (0.39), residues: 159 loop : 0.55 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.011 0.001 TYR A 474 PHE 0.013 0.001 PHE B 415 TRP 0.011 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13559) covalent geometry : angle 0.58435 / 0.30 (18459) hydrogen bonds : bond 0.03817 / 2.57 ( 647) hydrogen bonds : angle 4.41499 / 3.10 ( 1870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7555 (p-90) cc_final: 0.7059 (p-90) REVERT: A 634 ASP cc_start: 0.7139 (m-30) cc_final: 0.6878 (m-30) REVERT: A 660 ASP cc_start: 0.6794 (m-30) cc_final: 0.6393 (t0) REVERT: A 758 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: B 70 LEU cc_start: 0.8170 (tp) cc_final: 0.7863 (tp) REVERT: B 73 ASN cc_start: 0.7863 (m-40) cc_final: 0.7465 (m110) REVERT: B 87 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 126 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6424 (mp0) REVERT: B 169 ASP cc_start: 0.7223 (t0) cc_final: 0.6707 (m-30) REVERT: B 183 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7842 (t) REVERT: B 587 MET cc_start: 0.7356 (ttm) cc_final: 0.7084 (mtp) REVERT: B 834 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7644 (mmtp) outliers start: 29 outliers final: 15 residues processed: 194 average time/residue: 0.0977 time to fit residues: 28.8912 Evaluate side-chains 177 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135556 restraints weight = 17756.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136536 restraints weight = 16791.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137450 restraints weight = 14540.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137668 restraints weight = 12527.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138031 restraints weight = 11068.774| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13559 Z= 0.113 Angle : 0.564 11.211 18459 Z= 0.294 Chirality : 0.039 0.135 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.303 88.898 2185 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.27 % Allowed : 11.79 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1564 helix: 0.44 (0.17), residues: 888 sheet: 0.67 (0.39), residues: 166 loop : 0.62 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 873 TYR 0.016 0.001 TYR B 331 PHE 0.013 0.001 PHE A 432 TRP 0.020 0.001 TRP A 661 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (13559) covalent geometry : angle 0.56352 / 0.29 (18459) hydrogen bonds : bond 0.03500 / 2.35 ( 647) hydrogen bonds : angle 4.28227 / 3.00 ( 1870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7536 (p-90) cc_final: 0.7057 (p-90) REVERT: A 634 ASP cc_start: 0.7080 (m-30) cc_final: 0.6828 (m-30) REVERT: A 660 ASP cc_start: 0.6806 (m-30) cc_final: 0.6449 (t0) REVERT: A 758 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 768 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6376 (mtm-85) REVERT: B 70 LEU cc_start: 0.8151 (tp) cc_final: 0.7768 (tt) REVERT: B 73 ASN cc_start: 0.7849 (m-40) cc_final: 0.7547 (m110) REVERT: B 87 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7253 (t80) REVERT: B 169 ASP cc_start: 0.7235 (t0) cc_final: 0.6738 (m-30) REVERT: B 183 SER cc_start: 0.8229 (m) cc_final: 0.7850 (t) REVERT: B 316 MET cc_start: 0.7046 (ttm) cc_final: 0.6426 (ttm) REVERT: B 467 ARG cc_start: 0.6733 (mtt180) cc_final: 0.6437 (mtm180) REVERT: B 587 MET cc_start: 0.7334 (ttm) cc_final: 0.7106 (mtp) REVERT: B 834 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7643 (mmtp) REVERT: B 885 MET cc_start: 0.8242 (mtp) cc_final: 0.8012 (mtp) outliers start: 31 outliers final: 16 residues processed: 196 average time/residue: 0.0972 time to fit residues: 28.9997 Evaluate side-chains 177 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 647 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.0070 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS A 325 HIS B 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132992 restraints weight = 17721.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133257 restraints weight = 17207.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134071 restraints weight = 15918.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134493 restraints weight = 12849.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134894 restraints weight = 11620.452| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13559 Z= 0.153 Angle : 0.578 10.325 18459 Z= 0.302 Chirality : 0.041 0.167 2163 Planarity : 0.004 0.038 2189 Dihedral : 15.247 89.183 2185 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.49 % Allowed : 12.59 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1564 helix: 0.42 (0.17), residues: 889 sheet: 0.63 (0.40), residues: 161 loop : 0.49 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.014 0.001 TYR A 228 PHE 0.017 0.001 PHE A 765 TRP 0.013 0.001 TRP A 661 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13559) covalent geometry : angle 0.57763 / 0.30 (18459) hydrogen bonds : bond 0.03717 / 2.49 ( 647) hydrogen bonds : angle 4.27548 / 3.00 ( 1870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7549 (p-90) cc_final: 0.7027 (p-90) REVERT: A 429 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6585 (mt-10) REVERT: A 634 ASP cc_start: 0.7150 (m-30) cc_final: 0.6852 (m-30) REVERT: A 657 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: A 660 ASP cc_start: 0.6876 (m-30) cc_final: 0.6533 (t0) REVERT: A 758 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 768 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6397 (mtm-85) REVERT: B 73 ASN cc_start: 0.7878 (m-40) cc_final: 0.7554 (m110) REVERT: B 87 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7263 (t80) REVERT: B 169 ASP cc_start: 0.7295 (t0) cc_final: 0.6769 (m-30) REVERT: B 183 SER cc_start: 0.8214 (m) cc_final: 0.7822 (t) REVERT: B 587 MET cc_start: 0.7361 (ttm) cc_final: 0.7105 (mtp) REVERT: B 834 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7514 (mmtp) outliers start: 34 outliers final: 24 residues processed: 195 average time/residue: 0.0935 time to fit residues: 28.2067 Evaluate side-chains 183 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 592 ASN B 888 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.176238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134952 restraints weight = 17630.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134702 restraints weight = 16915.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.136002 restraints weight = 15535.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136141 restraints weight = 13014.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136748 restraints weight = 12207.611| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13559 Z= 0.121 Angle : 0.571 10.668 18459 Z= 0.297 Chirality : 0.040 0.142 2163 Planarity : 0.003 0.041 2189 Dihedral : 15.182 88.647 2185 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 13.62 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1564 helix: 0.57 (0.17), residues: 889 sheet: 0.64 (0.39), residues: 161 loop : 0.46 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.011 0.001 TYR A 331 PHE 0.011 0.001 PHE B 765 TRP 0.009 0.001 TRP A 74 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13559) covalent geometry : angle 0.57134 / 0.30 (18459) hydrogen bonds : bond 0.03428 / 2.31 ( 647) hydrogen bonds : angle 4.17173 / 2.92 ( 1870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7521 (p-90) cc_final: 0.7041 (p-90) REVERT: A 429 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 634 ASP cc_start: 0.7083 (m-30) cc_final: 0.6823 (m-30) REVERT: A 660 ASP cc_start: 0.6779 (m-30) cc_final: 0.6490 (t0) REVERT: A 758 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: A 768 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.6477 (mtm-85) REVERT: B 70 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7557 (tt) REVERT: B 73 ASN cc_start: 0.7788 (m-40) cc_final: 0.7457 (m110) REVERT: B 87 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 169 ASP cc_start: 0.7280 (t0) cc_final: 0.6785 (m-30) REVERT: B 183 SER cc_start: 0.8179 (m) cc_final: 0.7802 (t) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.1083 time to fit residues: 30.8197 Evaluate side-chains 179 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.172696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131484 restraints weight = 17719.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132157 restraints weight = 16721.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132900 restraints weight = 15735.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132896 restraints weight = 12894.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133129 restraints weight = 11739.117| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13559 Z= 0.197 Angle : 0.633 11.040 18459 Z= 0.328 Chirality : 0.042 0.153 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.255 88.493 2185 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.64 % Allowed : 14.20 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1564 helix: 0.38 (0.17), residues: 893 sheet: 0.48 (0.40), residues: 161 loop : 0.24 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.020 0.002 TYR A 228 PHE 0.023 0.002 PHE A 765 TRP 0.011 0.002 TRP A 666 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (13559) covalent geometry : angle 0.63265 / 0.33 (18459) hydrogen bonds : bond 0.03950 / 2.64 ( 647) hydrogen bonds : angle 4.32967 / 3.04 ( 1870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 634 ASP cc_start: 0.7163 (m-30) cc_final: 0.6876 (m-30) REVERT: A 660 ASP cc_start: 0.6790 (m-30) cc_final: 0.6489 (t0) REVERT: A 758 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: A 768 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.6593 (mtm-85) REVERT: B 70 LEU cc_start: 0.8161 (tt) cc_final: 0.7911 (tt) REVERT: B 87 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7174 (t80) REVERT: B 126 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 169 ASP cc_start: 0.7166 (t0) cc_final: 0.6705 (m-30) REVERT: B 183 SER cc_start: 0.8175 (m) cc_final: 0.7774 (t) outliers start: 36 outliers final: 27 residues processed: 188 average time/residue: 0.0959 time to fit residues: 27.6818 Evaluate side-chains 188 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133006 restraints weight = 17773.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132577 restraints weight = 16544.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133828 restraints weight = 15679.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134123 restraints weight = 13647.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134310 restraints weight = 12966.662| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13559 Z= 0.143 Angle : 0.595 11.111 18459 Z= 0.310 Chirality : 0.040 0.147 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.219 89.507 2185 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.49 % Allowed : 14.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1564 helix: 0.50 (0.17), residues: 894 sheet: 0.56 (0.40), residues: 159 loop : 0.20 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.011 0.001 TYR A 331 PHE 0.014 0.001 PHE A 432 TRP 0.010 0.001 TRP A 666 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13559) covalent geometry : angle 0.59506 / 0.31 (18459) hydrogen bonds : bond 0.03612 / 2.43 ( 647) hydrogen bonds : angle 4.21123 / 2.96 ( 1870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7564 (p-90) cc_final: 0.7003 (p-90) REVERT: A 429 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 634 ASP cc_start: 0.7083 (m-30) cc_final: 0.6822 (m-30) REVERT: A 660 ASP cc_start: 0.6758 (m-30) cc_final: 0.6523 (t0) REVERT: A 758 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: A 768 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.6519 (mtm-85) REVERT: B 70 LEU cc_start: 0.8173 (tt) cc_final: 0.7938 (tt) REVERT: B 87 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 126 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 169 ASP cc_start: 0.7125 (t0) cc_final: 0.6667 (m-30) REVERT: B 183 SER cc_start: 0.8191 (m) cc_final: 0.7790 (t) REVERT: B 753 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6779 (mm-40) outliers start: 34 outliers final: 25 residues processed: 188 average time/residue: 0.1068 time to fit residues: 30.6093 Evaluate side-chains 186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 135 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 73 ASN ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134775 restraints weight = 17724.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134905 restraints weight = 17145.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135691 restraints weight = 16528.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136337 restraints weight = 12919.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136394 restraints weight = 11862.551| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13559 Z= 0.116 Angle : 0.584 11.423 18459 Z= 0.303 Chirality : 0.039 0.144 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.151 88.836 2185 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.05 % Allowed : 14.86 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1564 helix: 0.67 (0.18), residues: 888 sheet: 0.55 (0.40), residues: 161 loop : 0.35 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 860 TYR 0.020 0.001 TYR B 331 PHE 0.013 0.001 PHE B 670 TRP 0.012 0.001 TRP A 349 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13559) covalent geometry : angle 0.58402 / 0.30 (18459) hydrogen bonds : bond 0.03367 / 2.27 ( 647) hydrogen bonds : angle 4.14439 / 2.90 ( 1870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7526 (p-90) cc_final: 0.6932 (p-90) REVERT: A 295 SER cc_start: 0.8253 (p) cc_final: 0.7821 (m) REVERT: A 429 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6765 (mt-10) REVERT: A 634 ASP cc_start: 0.7047 (m-30) cc_final: 0.6773 (m-30) REVERT: A 758 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: A 768 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.6500 (mtm-85) REVERT: B 70 LEU cc_start: 0.8150 (tt) cc_final: 0.7834 (tt) REVERT: B 87 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7218 (t80) REVERT: B 126 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: B 169 ASP cc_start: 0.7220 (t0) cc_final: 0.6768 (m-30) REVERT: B 183 SER cc_start: 0.8168 (m) cc_final: 0.7782 (t) outliers start: 28 outliers final: 22 residues processed: 187 average time/residue: 0.1039 time to fit residues: 29.8602 Evaluate side-chains 186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135413 restraints weight = 17646.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135270 restraints weight = 17151.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136349 restraints weight = 15929.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136795 restraints weight = 12341.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137058 restraints weight = 11236.797| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13559 Z= 0.116 Angle : 0.583 13.219 18459 Z= 0.301 Chirality : 0.039 0.143 2163 Planarity : 0.004 0.039 2189 Dihedral : 15.100 88.504 2185 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.98 % Allowed : 15.45 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1564 helix: 0.72 (0.17), residues: 888 sheet: 0.56 (0.40), residues: 161 loop : 0.37 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.014 0.001 TYR A 171 PHE 0.012 0.001 PHE B 670 TRP 0.012 0.001 TRP A 349 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13559) covalent geometry : angle 0.58262 / 0.30 (18459) hydrogen bonds : bond 0.03269 / 2.20 ( 647) hydrogen bonds : angle 4.12192 / 2.88 ( 1870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.22 seconds wall clock time: 33 minutes 31.96 seconds (2011.96 seconds total)