Starting phenix.real_space_refine on Fri Jul 3 08:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bha_44538/07_2026/9bha_44538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bha_44538/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bha_44538/07_2026/9bha_44538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bha_44538/07_2026/9bha_44538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bha_44538/07_2026/9bha_44538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bha_44538/07_2026/9bha_44538.map" } 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-dev-6108/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: 2.97, per 1000 atoms: 0.22 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: 1.03 Conformation dependent library (CDL) restraints added in 488.9 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: 1.46 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: 1.96 Time building geometry restraints manager: 1.29 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: 17893 1.74 - 3.49: 517 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: 3.180 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.900 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- 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 : 0.681 8.721 18459 Z= 0.457 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 0.68059 / 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 : 0.568 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: 0.8018 (tt) REVERT: B 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6632 (m-30) REVERT: B 678 THR cc_start: 0.8179 (p) cc_final: 0.7654 (t) REVERT: B 753 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7152 (mm-40) REVERT: B 855 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6026 (mp0) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1322 time to fit residues: 58.8557 Evaluate side-chains 171 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4238 r_free = 0.4238 target = 0.176529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135788 restraints weight = 17593.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135880 restraints weight = 17431.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136925 restraints weight = 16251.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137245 restraints weight = 13137.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137644 restraints weight = 11540.704| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13559 Z= 0.168 Angle : 0.678 11.014 18459 Z= 0.363 Chirality : 0.044 0.188 2163 Planarity : 0.005 0.042 2189 Dihedral : 15.737 89.844 2185 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.90 % Allowed : 7.83 % Favored : 90.26 % 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: -0.47 (0.20), residues: 1564 helix: -0.72 (0.16), residues: 887 sheet: 0.89 (0.39), residues: 145 loop : 0.47 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.017 0.002 TYR B 331 PHE 0.016 0.001 PHE B 415 TRP 0.017 0.002 TRP A 661 HIS 0.006 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (13559) covalent geometry : angle 0.67769 / 0.36 (18459) hydrogen bonds : bond 0.05190 / 3.46 ( 647) hydrogen bonds : angle 5.26612 / 3.69 ( 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 219 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8425 (tt) cc_final: 0.8131 (mm) REVERT: A 95 TRP cc_start: 0.7768 (p-90) cc_final: 0.7215 (p-90) REVERT: A 634 ASP cc_start: 0.7284 (m-30) cc_final: 0.7017 (m-30) REVERT: A 758 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: B 70 LEU cc_start: 0.8274 (tp) cc_final: 0.7760 (tt) REVERT: B 73 ASN cc_start: 0.7754 (m-40) cc_final: 0.7344 (m110) REVERT: B 169 ASP cc_start: 0.7122 (t0) cc_final: 0.6570 (m-30) REVERT: B 183 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7790 (t) REVERT: B 678 THR cc_start: 0.7968 (p) cc_final: 0.7553 (t) outliers start: 26 outliers final: 15 residues processed: 211 average time/residue: 0.1010 time to fit residues: 31.7012 Evaluate side-chains 182 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 183 SER Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 326 VAL 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: 8.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN B 592 ASN B 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134046 restraints weight = 18040.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134073 restraints weight = 17256.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135147 restraints weight = 15922.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135358 restraints weight = 12809.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135810 restraints weight = 11384.799| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2855 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= 0.150 Angle : 0.613 9.845 18459 Z= 0.326 Chirality : 0.042 0.171 2163 Planarity : 0.004 0.043 2189 Dihedral : 15.542 88.979 2185 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.90 % Allowed : 9.59 % Favored : 88.51 % 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: 0.00 (0.21), residues: 1564 helix: -0.22 (0.17), residues: 894 sheet: 0.72 (0.37), residues: 164 loop : 0.57 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.013 0.002 TYR B 331 PHE 0.015 0.001 PHE A 765 TRP 0.018 0.001 TRP A 661 HIS 0.012 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (13559) covalent geometry : angle 0.61262 / 0.33 (18459) hydrogen bonds : bond 0.04464 / 2.98 ( 647) hydrogen bonds : angle 4.76319 / 3.34 ( 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 211 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8355 (tt) cc_final: 0.8121 (mm) REVERT: A 95 TRP cc_start: 0.7594 (p-90) cc_final: 0.7077 (p-90) REVERT: A 634 ASP cc_start: 0.7222 (m-30) cc_final: 0.7019 (m-30) REVERT: A 660 ASP cc_start: 0.6818 (m-30) cc_final: 0.6378 (t0) REVERT: B 70 LEU cc_start: 0.8235 (tp) cc_final: 0.7683 (tt) REVERT: B 73 ASN cc_start: 0.7828 (m-40) cc_final: 0.7449 (m110) REVERT: B 87 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7261 (t80) REVERT: B 169 ASP cc_start: 0.7125 (t0) cc_final: 0.6555 (m-30) REVERT: B 183 SER cc_start: 0.8189 (m) cc_final: 0.7774 (t) REVERT: B 587 MET cc_start: 0.7379 (ttm) cc_final: 0.7092 (mtp) outliers start: 26 outliers final: 15 residues processed: 205 average time/residue: 0.0962 time to fit residues: 29.5677 Evaluate side-chains 174 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 134 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR 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: 0.9980 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133652 restraints weight = 18024.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134366 restraints weight = 17094.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135366 restraints weight = 15379.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135528 restraints weight = 12763.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136021 restraints weight = 11448.077| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13559 Z= 0.142 Angle : 0.600 12.004 18459 Z= 0.312 Chirality : 0.041 0.144 2163 Planarity : 0.004 0.037 2189 Dihedral : 15.431 89.238 2185 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.42 % Allowed : 10.40 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1564 helix: 0.04 (0.17), residues: 899 sheet: 0.74 (0.40), residues: 158 loop : 0.51 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 860 TYR 0.014 0.001 TYR A 474 PHE 0.014 0.001 PHE A 432 TRP 0.015 0.001 TRP A 661 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13559) covalent geometry : angle 0.59970 / 0.31 (18459) hydrogen bonds : bond 0.03909 / 2.63 ( 647) hydrogen bonds : angle 4.43806 / 3.12 ( 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 211 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7576 (p-90) cc_final: 0.7030 (p-90) REVERT: A 192 GLU cc_start: 0.7974 (mp0) cc_final: 0.7711 (mp0) REVERT: A 582 ILE cc_start: 0.8878 (mm) cc_final: 0.8608 (mt) REVERT: A 634 ASP cc_start: 0.7187 (m-30) cc_final: 0.6953 (m-30) REVERT: A 660 ASP cc_start: 0.6842 (m-30) cc_final: 0.6525 (t0) REVERT: A 758 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: B 70 LEU cc_start: 0.8188 (tp) cc_final: 0.7861 (tp) REVERT: B 73 ASN cc_start: 0.7905 (m-40) cc_final: 0.7519 (m110) REVERT: B 87 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7216 (t80) REVERT: B 169 ASP cc_start: 0.7196 (t0) cc_final: 0.6693 (m-30) REVERT: B 183 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 505 ILE cc_start: 0.8355 (pt) cc_final: 0.8110 (pt) REVERT: B 587 MET cc_start: 0.7373 (ttm) cc_final: 0.7105 (mtp) REVERT: B 885 MET cc_start: 0.8351 (mtp) cc_final: 0.8083 (mtp) outliers start: 33 outliers final: 16 residues processed: 200 average time/residue: 0.0869 time to fit residues: 26.8898 Evaluate side-chains 181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 492 SER 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 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 129 ILE 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 624 SER 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: 0.7980 chunk 68 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 592 ASN B 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133660 restraints weight = 17870.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134370 restraints weight = 16182.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134977 restraints weight = 15117.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135387 restraints weight = 12120.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135487 restraints weight = 10856.655| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13559 Z= 0.126 Angle : 0.561 10.186 18459 Z= 0.294 Chirality : 0.040 0.132 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.353 89.442 2185 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.05 % Allowed : 11.79 % Favored : 86.16 % 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: 0.50 (0.21), residues: 1564 helix: 0.33 (0.17), residues: 887 sheet: 0.69 (0.40), residues: 160 loop : 0.56 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.014 0.001 TYR B 331 PHE 0.013 0.001 PHE A 432 TRP 0.014 0.001 TRP A 661 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13559) covalent geometry : angle 0.56108 / 0.29 (18459) hydrogen bonds : bond 0.03646 / 2.45 ( 647) hydrogen bonds : angle 4.30183 / 3.01 ( 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 200 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7534 (p-90) cc_final: 0.7066 (p-90) REVERT: A 582 ILE cc_start: 0.8882 (mm) cc_final: 0.8602 (mt) REVERT: A 660 ASP cc_start: 0.6856 (m-30) cc_final: 0.6492 (t0) REVERT: A 758 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 768 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.6540 (mtm-85) REVERT: B 70 LEU cc_start: 0.8159 (tp) cc_final: 0.7768 (tt) REVERT: B 73 ASN cc_start: 0.7904 (m-40) cc_final: 0.7595 (m110) REVERT: B 87 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 169 ASP cc_start: 0.7284 (t0) cc_final: 0.6761 (m-30) REVERT: B 183 SER cc_start: 0.8210 (m) cc_final: 0.7821 (t) REVERT: B 316 MET cc_start: 0.7126 (ttm) cc_final: 0.6454 (ttm) REVERT: B 505 ILE cc_start: 0.8357 (pt) cc_final: 0.8099 (pt) REVERT: B 587 MET cc_start: 0.7352 (ttm) cc_final: 0.7100 (mtp) outliers start: 28 outliers final: 18 residues processed: 192 average time/residue: 0.0967 time to fit residues: 28.4191 Evaluate side-chains 178 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 326 VAL 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 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 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: 4.9990 chunk 102 optimal weight: 6.9990 chunk 137 optimal weight: 0.0170 chunk 143 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133685 restraints weight = 17764.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133537 restraints weight = 17183.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135415 restraints weight = 15360.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135636 restraints weight = 11784.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135930 restraints weight = 12083.703| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3570 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= 0.125 Angle : 0.559 10.400 18459 Z= 0.291 Chirality : 0.040 0.174 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.259 89.719 2185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.56 % Allowed : 11.86 % Favored : 85.58 % 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: 0.59 (0.21), residues: 1564 helix: 0.46 (0.17), residues: 888 sheet: 0.74 (0.40), residues: 155 loop : 0.48 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 873 TYR 0.012 0.001 TYR A 331 PHE 0.014 0.001 PHE A 432 TRP 0.012 0.001 TRP A 661 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13559) covalent geometry : angle 0.55855 / 0.29 (18459) hydrogen bonds : bond 0.03500 / 2.35 ( 647) hydrogen bonds : angle 4.24467 / 2.96 ( 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 201 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7546 (p-90) cc_final: 0.7075 (p-90) REVERT: A 582 ILE cc_start: 0.8859 (mm) cc_final: 0.8626 (mt) REVERT: A 660 ASP cc_start: 0.6888 (m-30) cc_final: 0.6554 (t0) REVERT: A 758 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: A 768 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.6501 (mtm-85) REVERT: B 70 LEU cc_start: 0.8210 (tp) cc_final: 0.7806 (tt) REVERT: B 73 ASN cc_start: 0.7834 (m-40) cc_final: 0.7522 (m110) REVERT: B 87 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7222 (t80) REVERT: B 169 ASP cc_start: 0.7284 (t0) cc_final: 0.6773 (m-30) REVERT: B 183 SER cc_start: 0.8228 (m) cc_final: 0.7840 (t) REVERT: B 505 ILE cc_start: 0.8282 (pt) cc_final: 0.8028 (pt) REVERT: B 587 MET cc_start: 0.7337 (ttm) cc_final: 0.7099 (mtp) outliers start: 35 outliers final: 24 residues processed: 191 average time/residue: 0.0969 time to fit residues: 28.6140 Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 421 THR 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 A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 123 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 592 ASN B 888 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134901 restraints weight = 17716.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135278 restraints weight = 16445.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135951 restraints weight = 15637.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136574 restraints weight = 12461.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136814 restraints weight = 11170.923| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13559 Z= 0.111 Angle : 0.543 10.633 18459 Z= 0.282 Chirality : 0.039 0.135 2163 Planarity : 0.003 0.042 2189 Dihedral : 15.191 88.593 2185 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.20 % Allowed : 13.25 % Favored : 84.55 % 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: 0.71 (0.21), residues: 1564 helix: 0.60 (0.17), residues: 895 sheet: 0.79 (0.40), residues: 153 loop : 0.43 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.015 0.001 TYR B 362 PHE 0.012 0.001 PHE A 432 TRP 0.012 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13559) covalent geometry : angle 0.54284 / 0.28 (18459) hydrogen bonds : bond 0.03314 / 2.25 ( 647) hydrogen bonds : angle 4.12419 / 2.89 ( 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 209 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7535 (p-90) cc_final: 0.7061 (p-90) REVERT: A 582 ILE cc_start: 0.8908 (mm) cc_final: 0.8659 (mt) REVERT: A 660 ASP cc_start: 0.6892 (m-30) cc_final: 0.6550 (t0) REVERT: A 758 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: A 768 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.6535 (mtm-85) REVERT: B 73 ASN cc_start: 0.7794 (m-40) cc_final: 0.7478 (m110) REVERT: B 87 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7192 (t80) REVERT: B 169 ASP cc_start: 0.7274 (t0) cc_final: 0.6800 (m-30) REVERT: B 183 SER cc_start: 0.8203 (m) cc_final: 0.7825 (t) REVERT: B 505 ILE cc_start: 0.8274 (pt) cc_final: 0.8028 (pt) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.0922 time to fit residues: 27.6839 Evaluate side-chains 195 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 270 ASN Chi-restraints excluded: chain A residue 326 VAL 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 B residue 87 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 172 MET 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 744 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 102 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 279 ASN B 596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132409 restraints weight = 17710.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133368 restraints weight = 16889.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133947 restraints weight = 15569.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134165 restraints weight = 12969.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134575 restraints weight = 11479.936| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13559 Z= 0.160 Angle : 0.601 11.150 18459 Z= 0.310 Chirality : 0.041 0.149 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.218 89.700 2185 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 0.59 (0.21), residues: 1564 helix: 0.55 (0.17), residues: 893 sheet: 0.66 (0.41), residues: 155 loop : 0.31 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 808 TYR 0.030 0.002 TYR B 331 PHE 0.018 0.001 PHE A 765 TRP 0.010 0.001 TRP A 666 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (13559) covalent geometry : angle 0.60073 / 0.31 (18459) hydrogen bonds : bond 0.03639 / 2.44 ( 647) hydrogen bonds : angle 4.19176 / 2.94 ( 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 204 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.8892 (mm) cc_final: 0.8640 (mt) REVERT: A 660 ASP cc_start: 0.6886 (m-30) cc_final: 0.6579 (t0) REVERT: A 758 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 768 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.6400 (mtm-85) REVERT: B 70 LEU cc_start: 0.8111 (tt) cc_final: 0.7688 (tt) REVERT: B 87 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7182 (t80) REVERT: B 169 ASP cc_start: 0.7135 (t0) cc_final: 0.6656 (m-30) REVERT: B 183 SER cc_start: 0.8192 (m) cc_final: 0.7788 (t) REVERT: B 316 MET cc_start: 0.6461 (ppp) cc_final: 0.6226 (tmm) REVERT: B 505 ILE cc_start: 0.8270 (pt) cc_final: 0.8011 (pt) REVERT: B 753 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6794 (mm-40) outliers start: 32 outliers final: 26 residues processed: 194 average time/residue: 0.0957 time to fit residues: 28.6229 Evaluate side-chains 191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 270 ASN Chi-restraints excluded: chain A residue 317 LEU 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 590 LEU 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 A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 123 LEU 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 744 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134362 restraints weight = 17777.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134497 restraints weight = 16896.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135707 restraints weight = 15228.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136003 restraints weight = 12369.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136227 restraints weight = 11848.424| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3912 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= 0.119 Angle : 0.569 11.113 18459 Z= 0.295 Chirality : 0.039 0.143 2163 Planarity : 0.003 0.039 2189 Dihedral : 15.171 89.285 2185 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.98 % Allowed : 14.49 % Favored : 83.53 % 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: 0.70 (0.18), residues: 893 sheet: 0.61 (0.39), residues: 159 loop : 0.38 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 808 TYR 0.025 0.001 TYR B 331 PHE 0.015 0.001 PHE B 670 TRP 0.012 0.001 TRP A 661 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13559) covalent geometry : angle 0.56853 / 0.29 (18459) hydrogen bonds : bond 0.03324 / 2.24 ( 647) hydrogen bonds : angle 4.09607 / 2.87 ( 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 195 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7554 (p-90) cc_final: 0.6967 (p-90) REVERT: A 295 SER cc_start: 0.8316 (p) cc_final: 0.7896 (m) REVERT: A 582 ILE cc_start: 0.8875 (mm) cc_final: 0.8645 (mt) REVERT: A 657 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: A 660 ASP cc_start: 0.6806 (m-30) cc_final: 0.6580 (t0) REVERT: A 758 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 768 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.6554 (mtm-85) REVERT: B 87 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7191 (t80) REVERT: B 169 ASP cc_start: 0.7225 (t0) cc_final: 0.6770 (m-30) REVERT: B 183 SER cc_start: 0.8187 (m) cc_final: 0.7800 (t) REVERT: B 316 MET cc_start: 0.6235 (ppp) cc_final: 0.5955 (tmm) REVERT: B 505 ILE cc_start: 0.8226 (pt) cc_final: 0.7955 (pt) outliers start: 27 outliers final: 21 residues processed: 187 average time/residue: 0.0987 time to fit residues: 28.1920 Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 270 ASN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 VAL 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 B residue 87 PHE Chi-restraints excluded: chain B residue 123 LEU 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 744 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.176999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136112 restraints weight = 17715.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137730 restraints weight = 16509.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138169 restraints weight = 15092.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138335 restraints weight = 12047.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138322 restraints weight = 11517.427| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13559 Z= 0.108 Angle : 0.564 11.447 18459 Z= 0.292 Chirality : 0.039 0.143 2163 Planarity : 0.003 0.039 2189 Dihedral : 15.115 88.307 2185 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.83 % Allowed : 14.71 % Favored : 83.46 % 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: 0.89 (0.21), residues: 1564 helix: 0.83 (0.18), residues: 887 sheet: 0.64 (0.40), residues: 160 loop : 0.40 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 808 TYR 0.015 0.001 TYR B 331 PHE 0.012 0.001 PHE B 670 TRP 0.016 0.001 TRP A 349 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13559) covalent geometry : angle 0.56374 / 0.29 (18459) hydrogen bonds : bond 0.03154 / 2.11 ( 647) hydrogen bonds : angle 4.02439 / 2.82 ( 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 190 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7539 (p-90) cc_final: 0.6957 (p-90) REVERT: A 295 SER cc_start: 0.8268 (p) cc_final: 0.7914 (m) REVERT: A 582 ILE cc_start: 0.8884 (mm) cc_final: 0.8654 (mt) REVERT: A 758 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 768 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6564 (mtm-85) REVERT: B 70 LEU cc_start: 0.8155 (tt) cc_final: 0.7919 (pt) REVERT: B 87 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 169 ASP cc_start: 0.7216 (t0) cc_final: 0.6758 (m-30) REVERT: B 183 SER cc_start: 0.8155 (m) cc_final: 0.7771 (t) REVERT: B 505 ILE cc_start: 0.8197 (pt) cc_final: 0.7919 (pt) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.1040 time to fit residues: 29.0436 Evaluate side-chains 181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain A residue 326 VAL 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 B residue 87 PHE Chi-restraints excluded: chain B residue 123 LEU 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 744 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.175360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133841 restraints weight = 17713.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134277 restraints weight = 17691.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135139 restraints weight = 16045.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135661 restraints weight = 12899.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135682 restraints weight = 12267.238| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13559 Z= 0.136 Angle : 0.588 13.326 18459 Z= 0.303 Chirality : 0.040 0.145 2163 Planarity : 0.004 0.039 2189 Dihedral : 15.120 89.541 2185 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.49 % Allowed : 14.35 % 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: 0.75 (0.21), residues: 1564 helix: 0.72 (0.17), residues: 893 sheet: 0.66 (0.40), residues: 159 loop : 0.30 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.015 0.001 TYR A 331 PHE 0.014 0.001 PHE A 765 TRP 0.013 0.001 TRP A 349 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13559) covalent geometry : angle 0.58809 / 0.30 (18459) hydrogen bonds : bond 0.03316 / 2.22 ( 647) hydrogen bonds : angle 4.03424 / 2.83 ( 1870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.86 seconds wall clock time: 33 minutes 20.58 seconds (2000.58 seconds total)