Starting phenix.real_space_refine on Sat Aug 23 16:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bha_44538/08_2025/9bha_44538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bha_44538/08_2025/9bha_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_44538/08_2025/9bha_44538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2025/9bha_44538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2025/9bha_44538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bha_44538/08_2025/9bha_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-2.0-5787/lib/python3.9/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: 3.76, per 1000 atoms: 0.28 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: 1.21 Conformation dependent library (CDL) restraints added in 605.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.75 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: 2.58 Time building geometry restraints manager: 1.56 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=" C4' DA Y 40 " pdb=" O4' DA Y 40 " ideal model delta sigma weight residual 1.450 1.423 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C3' DA Y 40 " pdb=" C2' DA Y 40 " ideal model delta sigma weight residual 1.525 1.548 -0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.525 1.548 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" O4' DG Y 36 " pdb=" C1' DG Y 36 " ideal model delta sigma weight residual 1.414 1.392 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C4' DT Y 39 " pdb=" O4' DT Y 39 " ideal model delta sigma weight residual 1.450 1.429 0.021 2.00e-02 2.50e+03 1.06e+00 ... (remaining 13554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 17958 1.74 - 3.49: 467 3.49 - 5.23: 32 5.23 - 6.98: 1 6.98 - 8.72: 1 Bond angle restraints: 18459 Sorted by residual: angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 109.70 105.55 4.15 1.50e+00 4.44e-01 7.65e+00 angle pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " pdb=" CG LEU A 233 " ideal model delta sigma weight residual 116.30 125.02 -8.72 3.50e+00 8.16e-02 6.21e+00 angle pdb=" C2' DG Y 21 " pdb=" C1' DG Y 21 " pdb=" N9 DG Y 21 " ideal model delta sigma weight residual 113.50 117.22 -3.72 1.50e+00 4.44e-01 6.16e+00 angle pdb=" O3' DG X 50 " pdb=" P DC X 51 " pdb=" O5' DC X 51 " ideal model delta sigma weight residual 104.00 107.68 -3.68 1.50e+00 4.44e-01 6.03e+00 angle pdb=" C2' DT Y 39 " pdb=" C1' DT Y 39 " pdb=" N1 DT Y 39 " ideal model delta sigma weight residual 113.50 117.13 -3.63 1.50e+00 4.44e-01 5.86e+00 ... (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 - 0.039: 1444 0.039 - 0.078: 551 0.078 - 0.117: 132 0.117 - 0.156: 33 0.156 - 0.195: 3 Chirality restraints: 2163 Sorted by residual: 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' 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 -0.19 2.00e-01 2.50e+01 9.13e-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 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 2160 not shown) Planarity restraints: 2189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 39 " -0.045 2.00e-02 2.50e+03 3.27e-02 2.68e+01 pdb=" N1 DT Y 39 " 0.087 2.00e-02 2.50e+03 pdb=" C2 DT Y 39 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DT Y 39 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT Y 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT Y 39 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT Y 39 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT Y 39 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT Y 39 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT Y 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 35 " -0.036 2.00e-02 2.50e+03 2.54e-02 1.77e+01 pdb=" N9 DA Y 35 " 0.071 2.00e-02 2.50e+03 pdb=" C8 DA Y 35 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DA Y 35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA Y 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA Y 35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA Y 35 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA Y 35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA Y 35 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA Y 35 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA Y 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 22 " 0.025 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" N1 DT Y 22 " -0.061 2.00e-02 2.50e+03 pdb=" C2 DT Y 22 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DT Y 22 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT Y 22 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT Y 22 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT Y 22 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT Y 22 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT Y 22 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT Y 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 2186 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4199 2.85 - 3.37: 12597 3.37 - 3.88: 20600 3.88 - 4.39: 25175 4.39 - 4.90: 41596 Nonbonded interactions: 104167 Sorted by model distance: nonbonded pdb=" OG1 THR A 655 " pdb=" OG SER A 722 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASP B 634 " pdb=" NH2 ARG B 711 " model vdw 2.344 3.120 nonbonded pdb=" OD2 ASP A 727 " pdb=" OH TYR A 741 " model vdw 2.389 3.040 nonbonded pdb=" OH TYR B 113 " pdb=" O LYS B 121 " model vdw 2.394 3.040 nonbonded pdb=" OD1 ASN B 773 " pdb=" N MET B 774 " model vdw 2.404 3.120 ... (remaining 104162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 566 or resid 577 through 863 or resid 870 throu \ gh 892)) selection = (chain 'B' and (resid 67 through 600 or resid 605 through 892)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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= 0.131 Angle : 0.655 8.721 18459 Z= 0.393 Chirality : 0.044 0.195 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 aren 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 covalent geometry : bond 0.00279 (13559) covalent geometry : angle 0.65499 (18459) hydrogen bonds : bond 0.20393 ( 647) hydrogen bonds : angle 8.16642 ( 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 : 0.505 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: 0.7209 (p-90) REVERT: A 446 LEU cc_start: 0.6996 (mt) cc_final: 0.6755 (mt) REVERT: B 70 LEU cc_start: 0.8279 (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: 0.8178 (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: 0.1518 time to fit residues: 66.7039 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 : 0.608 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 284 HIS A 325 HIS A 366 HIS A 649 HIS A 738 ASN B 219 HIS B 284 HIS B 384 GLN B 636 GLN B 738 ASN B 780 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136574 restraints weight = 17562.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136798 restraints weight = 16933.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137647 restraints weight = 16085.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137781 restraints weight = 12927.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138104 restraints weight = 11563.868| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2846 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= 0.148 Angle : 0.612 10.102 18459 Z= 0.328 Chirality : 0.041 0.200 2163 Planarity : 0.004 0.039 2189 Dihedral : 15.421 88.057 2185 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.68 % Allowed : 8.20 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.20), residues: 1564 helix: -0.44 (0.16), residues: 895 sheet: 1.05 (0.38), residues: 163 loop : 0.51 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 696 TYR 0.011 0.001 TYR B 362 PHE 0.017 0.001 PHE B 415 TRP 0.020 0.002 TRP A 74 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00339 (13559) covalent geometry : angle 0.61180 (18459) hydrogen bonds : bond 0.04143 ( 647) hydrogen bonds : angle 4.77278 ( 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 246 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7603 (p-90) cc_final: 0.7060 (p-90) REVERT: A 634 ASP cc_start: 0.6980 (m-30) cc_final: 0.6751 (m-30) REVERT: A 660 ASP cc_start: 0.6773 (m-30) cc_final: 0.6318 (t0) REVERT: A 758 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 70 LEU cc_start: 0.8253 (tp) cc_final: 0.7638 (tt) REVERT: B 73 ASN cc_start: 0.7738 (m-40) cc_final: 0.7357 (m110) REVERT: B 87 PHE cc_start: 0.7456 (m-80) cc_final: 0.7240 (m-10) REVERT: B 126 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: B 169 ASP cc_start: 0.7151 (t0) cc_final: 0.6645 (m-30) REVERT: B 183 SER cc_start: 0.8131 (m) cc_final: 0.7802 (t) REVERT: B 678 THR cc_start: 0.7979 (p) cc_final: 0.7617 (t) outliers start: 23 outliers final: 12 residues processed: 240 average time/residue: 0.1193 time to fit residues: 41.9017 Evaluate side-chains 193 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 126 GLU Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 612 THR 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: 0.0770 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 HIS A 363 ASN B 284 HIS B 338 HIS B 592 ASN B 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.174992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133514 restraints weight = 17812.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133649 restraints weight = 16930.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134978 restraints weight = 15117.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.134937 restraints weight = 12721.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135358 restraints weight = 11212.596| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3374 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= 0.137 Angle : 0.581 8.555 18459 Z= 0.306 Chirality : 0.040 0.150 2163 Planarity : 0.004 0.038 2189 Dihedral : 15.283 89.802 2185 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.05 % Allowed : 10.32 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.21), residues: 1564 helix: 0.12 (0.17), residues: 901 sheet: 1.04 (0.40), residues: 158 loop : 0.53 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 735 TYR 0.012 0.001 TYR B 283 PHE 0.013 0.001 PHE B 415 TRP 0.013 0.001 TRP A 74 HIS 0.014 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00319 (13559) covalent geometry : angle 0.58133 (18459) hydrogen bonds : bond 0.03754 ( 647) hydrogen bonds : angle 4.38441 ( 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 215 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7552 (p-90) cc_final: 0.7042 (p-90) REVERT: A 582 ILE cc_start: 0.8932 (mm) cc_final: 0.8677 (mt) REVERT: A 657 MET cc_start: 0.7356 (tpp) cc_final: 0.7077 (mpp) REVERT: A 660 ASP cc_start: 0.6776 (m-30) cc_final: 0.6405 (t0) REVERT: A 680 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7356 (mtt) REVERT: A 758 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: B 70 LEU cc_start: 0.8183 (tp) cc_final: 0.7548 (tt) REVERT: B 73 ASN cc_start: 0.7941 (m-40) cc_final: 0.7517 (m110) REVERT: B 126 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: B 137 ARG cc_start: 0.6957 (mmm160) cc_final: 0.6634 (mmp-170) REVERT: B 169 ASP cc_start: 0.7165 (t0) cc_final: 0.6678 (m-30) REVERT: B 183 SER cc_start: 0.8209 (m) cc_final: 0.7819 (t) REVERT: B 331 TYR cc_start: 0.6720 (t80) cc_final: 0.6472 (t80) outliers start: 28 outliers final: 17 residues processed: 205 average time/residue: 0.1077 time to fit residues: 32.8821 Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 680 MET 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 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 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 647 ASP Chi-restraints excluded: chain B residue 662 THR 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: 2.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 0.0070 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 325 HIS B 596 GLN B 888 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.178598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137629 restraints weight = 17779.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138066 restraints weight = 16335.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139388 restraints weight = 14481.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139657 restraints weight = 11691.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139742 restraints weight = 11133.038| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13559 Z= 0.105 Angle : 0.523 9.021 18459 Z= 0.274 Chirality : 0.038 0.132 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.174 87.894 2185 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.61 % Allowed : 12.45 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1564 helix: 0.65 (0.17), residues: 894 sheet: 0.99 (0.40), residues: 155 loop : 0.61 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 823 TYR 0.013 0.001 TYR B 362 PHE 0.013 0.001 PHE A 432 TRP 0.019 0.001 TRP A 661 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00228 (13559) covalent geometry : angle 0.52273 (18459) hydrogen bonds : bond 0.02995 ( 647) hydrogen bonds : angle 4.01596 ( 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 218 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7539 (p-90) cc_final: 0.7055 (p-90) REVERT: A 207 MET cc_start: 0.8843 (tpt) cc_final: 0.8122 (mmt) REVERT: A 467 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7429 (mmt-90) REVERT: A 582 ILE cc_start: 0.8923 (mm) cc_final: 0.8639 (mt) REVERT: A 660 ASP cc_start: 0.6727 (m-30) cc_final: 0.6352 (t0) REVERT: A 758 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 768 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6736 (mtm-85) REVERT: B 73 ASN cc_start: 0.7829 (m-40) cc_final: 0.7597 (m110) REVERT: B 126 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6423 (mp0) REVERT: B 169 ASP cc_start: 0.7129 (t0) cc_final: 0.6644 (m-30) REVERT: B 183 SER cc_start: 0.8210 (m) cc_final: 0.7826 (t) REVERT: B 392 ASP cc_start: 0.7017 (m-30) cc_final: 0.6808 (m-30) REVERT: B 505 ILE cc_start: 0.8295 (pt) cc_final: 0.8088 (pt) REVERT: B 775 GLU cc_start: 0.8234 (tt0) cc_final: 0.7748 (tt0) outliers start: 22 outliers final: 13 residues processed: 210 average time/residue: 0.1024 time to fit residues: 31.5847 Evaluate side-chains 184 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER 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: 1.9990 chunk 68 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 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 = 0.4244 r_free = 0.4244 target = 0.176982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135792 restraints weight = 17813.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135827 restraints weight = 16496.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136876 restraints weight = 15316.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137358 restraints weight = 11919.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137384 restraints weight = 11482.164| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13559 Z= 0.121 Angle : 0.541 9.251 18459 Z= 0.282 Chirality : 0.039 0.132 2163 Planarity : 0.003 0.037 2189 Dihedral : 15.148 89.321 2185 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.12 % Allowed : 12.45 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1564 helix: 0.77 (0.18), residues: 899 sheet: 1.12 (0.40), residues: 153 loop : 0.46 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.009 0.001 TYR A 331 PHE 0.012 0.001 PHE B 765 TRP 0.012 0.001 TRP A 863 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00280 (13559) covalent geometry : angle 0.54142 (18459) hydrogen bonds : bond 0.03245 ( 647) hydrogen bonds : angle 3.94656 ( 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 205 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7567 (p-90) cc_final: 0.7002 (p-90) REVERT: A 193 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7384 (mmm160) REVERT: A 207 MET cc_start: 0.8811 (tpt) cc_final: 0.8130 (mmt) REVERT: A 423 GLU cc_start: 0.7139 (tp30) cc_final: 0.6062 (pm20) REVERT: A 467 ARG cc_start: 0.7702 (mmt180) cc_final: 0.7428 (mmt-90) REVERT: A 582 ILE cc_start: 0.8908 (mm) cc_final: 0.8663 (mt) REVERT: A 657 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7074 (mtp) REVERT: A 660 ASP cc_start: 0.6714 (m-30) cc_final: 0.6422 (t0) REVERT: A 758 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: A 768 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.6741 (mtm-85) REVERT: B 126 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6353 (mp0) REVERT: B 169 ASP cc_start: 0.7231 (t0) cc_final: 0.6780 (m-30) REVERT: B 183 SER cc_start: 0.8178 (m) cc_final: 0.7785 (t) REVERT: B 316 MET cc_start: 0.6296 (tmm) cc_final: 0.5940 (tmm) REVERT: B 392 ASP cc_start: 0.6775 (m-30) cc_final: 0.6574 (m-30) REVERT: B 505 ILE cc_start: 0.8291 (pt) cc_final: 0.8008 (pt) REVERT: B 753 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6747 (mm-40) REVERT: B 775 GLU cc_start: 0.8194 (tt0) cc_final: 0.7750 (tt0) outliers start: 29 outliers final: 21 residues processed: 194 average time/residue: 0.1060 time to fit residues: 29.9072 Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 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 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 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 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4232 r_free = 0.4232 target = 0.175973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135072 restraints weight = 17752.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135507 restraints weight = 16962.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136387 restraints weight = 16285.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136630 restraints weight = 13158.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136725 restraints weight = 12257.145| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4239 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= 0.131 Angle : 0.539 9.667 18459 Z= 0.281 Chirality : 0.039 0.133 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.061 88.640 2185 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.27 % Allowed : 13.10 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1564 helix: 0.83 (0.18), residues: 898 sheet: 1.08 (0.41), residues: 154 loop : 0.36 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.015 0.001 TYR B 362 PHE 0.013 0.001 PHE B 765 TRP 0.010 0.001 TRP A 666 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00309 (13559) covalent geometry : angle 0.53947 (18459) hydrogen bonds : bond 0.03300 ( 647) hydrogen bonds : angle 3.92762 ( 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 200 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.8830 (tpt) cc_final: 0.8133 (mmt) REVERT: A 423 GLU cc_start: 0.7188 (tp30) cc_final: 0.6164 (pm20) REVERT: A 467 ARG cc_start: 0.7620 (mmt180) cc_final: 0.7363 (mmt-90) REVERT: A 582 ILE cc_start: 0.8903 (mm) cc_final: 0.8680 (mt) REVERT: A 590 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 758 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 768 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.6712 (mtm-85) REVERT: A 825 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6612 (t0) REVERT: B 169 ASP cc_start: 0.7222 (t0) cc_final: 0.6799 (m-30) REVERT: B 183 SER cc_start: 0.8163 (m) cc_final: 0.7770 (t) REVERT: B 316 MET cc_start: 0.6555 (tmm) cc_final: 0.6093 (tmm) REVERT: B 753 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6715 (mm-40) REVERT: B 775 GLU cc_start: 0.8148 (tt0) cc_final: 0.7676 (tt0) outliers start: 31 outliers final: 21 residues processed: 188 average time/residue: 0.1145 time to fit residues: 31.8751 Evaluate side-chains 187 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 436 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 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 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 = 0.4194 r_free = 0.4194 target = 0.172553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130586 restraints weight = 17822.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131750 restraints weight = 17787.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132371 restraints weight = 15575.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132813 restraints weight = 13158.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132749 restraints weight = 12223.705| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13559 Z= 0.178 Angle : 0.589 10.269 18459 Z= 0.307 Chirality : 0.041 0.155 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.220 86.837 2185 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.42 % Allowed : 13.69 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1564 helix: 0.62 (0.17), residues: 895 sheet: 0.80 (0.41), residues: 156 loop : 0.36 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.014 0.002 TYR A 171 PHE 0.016 0.001 PHE A 765 TRP 0.012 0.001 TRP A 661 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00428 (13559) covalent geometry : angle 0.58921 (18459) hydrogen bonds : bond 0.03749 ( 647) hydrogen bonds : angle 4.08769 ( 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 192 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.8935 (tpt) cc_final: 0.8208 (mmt) REVERT: A 293 LEU cc_start: 0.8263 (mm) cc_final: 0.8043 (tt) REVERT: A 582 ILE cc_start: 0.8932 (mm) cc_final: 0.8718 (mt) REVERT: A 590 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 758 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: A 768 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6405 (mtm-85) REVERT: B 169 ASP cc_start: 0.7128 (t0) cc_final: 0.6696 (m-30) REVERT: B 183 SER cc_start: 0.8211 (m) cc_final: 0.7781 (t) REVERT: B 753 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6733 (mm-40) REVERT: B 775 GLU cc_start: 0.8242 (tt0) cc_final: 0.7875 (tt0) outliers start: 33 outliers final: 25 residues processed: 180 average time/residue: 0.1224 time to fit residues: 32.6423 Evaluate side-chains 178 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 436 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 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR 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: 4.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 0.0030 chunk 5 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132401 restraints weight = 17780.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132042 restraints weight = 17357.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133142 restraints weight = 17303.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133445 restraints weight = 13519.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133663 restraints weight = 12817.203| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13559 Z= 0.166 Angle : 0.587 12.374 18459 Z= 0.303 Chirality : 0.040 0.171 2163 Planarity : 0.004 0.043 2189 Dihedral : 15.260 88.274 2185 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 14.71 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.21), residues: 1564 helix: 0.62 (0.17), residues: 889 sheet: 0.76 (0.41), residues: 154 loop : 0.24 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 808 TYR 0.016 0.002 TYR B 362 PHE 0.013 0.001 PHE B 765 TRP 0.010 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00397 (13559) covalent geometry : angle 0.58683 (18459) hydrogen bonds : bond 0.03588 ( 647) hydrogen bonds : angle 4.09925 ( 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 194 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.8932 (tpt) cc_final: 0.8155 (mmt) REVERT: A 493 ILE cc_start: 0.8638 (mt) cc_final: 0.8398 (mt) REVERT: A 590 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 758 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: A 768 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.6631 (mtm-85) REVERT: B 169 ASP cc_start: 0.7129 (t0) cc_final: 0.6722 (m-30) REVERT: B 183 SER cc_start: 0.8189 (m) cc_final: 0.7749 (t) REVERT: B 753 GLN cc_start: 0.7018 (mm-40) cc_final: 0.6776 (mm-40) REVERT: B 775 GLU cc_start: 0.8167 (tt0) cc_final: 0.7753 (tt0) outliers start: 31 outliers final: 25 residues processed: 183 average time/residue: 0.1164 time to fit residues: 32.0800 Evaluate side-chains 178 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 436 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 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 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 = 0.4233 r_free = 0.4233 target = 0.176180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135183 restraints weight = 17742.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135148 restraints weight = 16960.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136365 restraints weight = 15210.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136749 restraints weight = 12098.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136798 restraints weight = 11624.950| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13559 Z= 0.118 Angle : 0.561 13.365 18459 Z= 0.287 Chirality : 0.038 0.162 2163 Planarity : 0.004 0.044 2189 Dihedral : 15.115 87.749 2185 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.90 % Allowed : 15.37 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.21), residues: 1564 helix: 0.90 (0.18), residues: 879 sheet: 0.78 (0.41), residues: 156 loop : 0.27 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 808 TYR 0.015 0.001 TYR B 331 PHE 0.012 0.001 PHE B 765 TRP 0.010 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00273 (13559) covalent geometry : angle 0.56147 (18459) hydrogen bonds : bond 0.03092 ( 647) hydrogen bonds : angle 3.91879 ( 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 191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.462 Fit side-chains REVERT: A 423 GLU cc_start: 0.7120 (tp30) cc_final: 0.6080 (pm20) REVERT: A 493 ILE cc_start: 0.8586 (mt) cc_final: 0.8365 (mt) REVERT: A 590 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 758 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: A 768 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6746 (mtm-85) REVERT: B 169 ASP cc_start: 0.7233 (t0) cc_final: 0.6817 (m-30) REVERT: B 183 SER cc_start: 0.8202 (m) cc_final: 0.7746 (t) REVERT: B 505 ILE cc_start: 0.8253 (pt) cc_final: 0.7896 (pt) REVERT: B 586 VAL cc_start: 0.8651 (t) cc_final: 0.8365 (p) outliers start: 26 outliers final: 19 residues processed: 181 average time/residue: 0.1115 time to fit residues: 29.8558 Evaluate side-chains 175 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 582 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG 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 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 135 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 122 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137256 restraints weight = 17754.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137479 restraints weight = 16802.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138763 restraints weight = 15042.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139056 restraints weight = 11986.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139270 restraints weight = 11763.146| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13559 Z= 0.107 Angle : 0.553 13.776 18459 Z= 0.283 Chirality : 0.038 0.153 2163 Planarity : 0.003 0.043 2189 Dihedral : 15.029 86.588 2185 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.54 % Allowed : 15.81 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1564 helix: 1.07 (0.18), residues: 876 sheet: 0.90 (0.41), residues: 151 loop : 0.38 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 808 TYR 0.016 0.001 TYR B 362 PHE 0.012 0.001 PHE B 765 TRP 0.011 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00241 (13559) covalent geometry : angle 0.55271 (18459) hydrogen bonds : bond 0.02906 ( 647) hydrogen bonds : angle 3.85147 ( 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 184 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 493 ILE cc_start: 0.8613 (mt) cc_final: 0.8379 (mt) REVERT: A 590 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 758 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: A 768 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: A 825 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6491 (t0) REVERT: B 169 ASP cc_start: 0.7182 (t0) cc_final: 0.6780 (m-30) REVERT: B 183 SER cc_start: 0.8172 (m) cc_final: 0.7727 (t) REVERT: B 505 ILE cc_start: 0.8253 (pt) cc_final: 0.7912 (pt) REVERT: B 586 VAL cc_start: 0.8497 (t) cc_final: 0.8189 (p) outliers start: 21 outliers final: 17 residues processed: 174 average time/residue: 0.1151 time to fit residues: 29.8597 Evaluate side-chains 175 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 582 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG 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 102 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 145 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.177273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136536 restraints weight = 17633.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136528 restraints weight = 16749.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137873 restraints weight = 15296.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138222 restraints weight = 11973.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138400 restraints weight = 11479.309| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4906 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= 0.113 Angle : 0.558 14.126 18459 Z= 0.286 Chirality : 0.038 0.154 2163 Planarity : 0.004 0.044 2189 Dihedral : 15.017 87.780 2185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 16.33 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.22), residues: 1564 helix: 1.13 (0.18), residues: 874 sheet: 0.92 (0.41), residues: 156 loop : 0.38 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 808 TYR 0.017 0.001 TYR A 331 PHE 0.012 0.001 PHE B 765 TRP 0.010 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00259 (13559) covalent geometry : angle 0.55818 (18459) hydrogen bonds : bond 0.02962 ( 647) hydrogen bonds : angle 3.84593 ( 1870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.17 seconds wall clock time: 36 minutes 21.88 seconds (2181.88 seconds total)