Starting phenix.real_space_refine on Wed Jun 11 20:29:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bha_44538/06_2025/9bha_44538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bha_44538/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bha_44538/06_2025/9bha_44538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bha_44538/06_2025/9bha_44538.map" model { file = "/net/cci-nas-00/data/ceres_data/9bha_44538/06_2025/9bha_44538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bha_44538/06_2025/9bha_44538.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3, ' DC:plan': 1, ' DT:plan': 1} 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: {' DG:plan': 5, ' DG:plan2': 5, ' DC:plan2': 5, ' DA:plan2': 1, ' DC%5*END:plan2': 1, ' DC:plan': 5, ' DC%5*END:plan': 1, ' DT:plan': 8, ' DA:plan': 1} Unresolved non-hydrogen planarities: 209 Time building chain proxies: 8.27, per 1000 atoms: 0.62 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.07 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: 4.21 Time building geometry restraints manager: 3.54 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: 2.170 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.360 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP B 666 HIS 0.007 0.001 HIS A 366 PHE 0.020 0.001 PHE B 658 TYR 0.024 0.005 TYR A 239 ARG 0.018 0.003 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.20393 ( 647) hydrogen bonds : angle 8.16642 ( 1870) covalent geometry : bond 0.00279 (13559) covalent geometry : angle 0.65499 (18459) *********************** 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 : 1.488 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: 0.7228 (p-90) REVERT: A 446 LEU cc_start: 0.6996 (mt) cc_final: 0.6756 (mt) REVERT: B 70 LEU cc_start: 0.8279 (tp) cc_final: 0.8019 (tt) REVERT: B 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6633 (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: 0.6030 (mp0) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.3083 time to fit residues: 135.7100 Evaluate side-chains 174 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.7980 chunk 122 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 0.0060 chunk 147 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.179553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138587 restraints weight = 17578.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139503 restraints weight = 16708.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140521 restraints weight = 14621.818| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13559 Z= 0.133 Angle : 0.597 9.772 18459 Z= 0.321 Chirality : 0.041 0.190 2163 Planarity : 0.004 0.043 2189 Dihedral : 15.357 88.986 2185 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.46 % Allowed : 7.98 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1564 helix: -0.31 (0.16), residues: 897 sheet: 1.13 (0.38), residues: 163 loop : 0.59 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 74 HIS 0.005 0.001 HIS A 366 PHE 0.017 0.001 PHE B 415 TYR 0.012 0.001 TYR B 362 ARG 0.005 0.001 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 647) hydrogen bonds : angle 4.70780 ( 1870) covalent geometry : bond 0.00288 (13559) covalent geometry : angle 0.59679 (18459) *********************** 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 250 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7532 (p-90) cc_final: 0.7080 (p-90) REVERT: A 423 GLU cc_start: 0.7225 (tp30) cc_final: 0.6103 (pm20) REVERT: A 634 ASP cc_start: 0.6860 (m-30) cc_final: 0.6637 (m-30) REVERT: A 660 ASP cc_start: 0.6645 (m-30) cc_final: 0.6277 (t0) REVERT: A 758 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: B 70 LEU cc_start: 0.8226 (tp) cc_final: 0.7638 (tt) REVERT: B 73 ASN cc_start: 0.7732 (m-40) cc_final: 0.7315 (m110) REVERT: B 87 PHE cc_start: 0.7459 (m-80) cc_final: 0.7237 (m-10) REVERT: B 126 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 169 ASP cc_start: 0.7158 (t0) cc_final: 0.6616 (m-30) REVERT: B 183 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7810 (t) REVERT: B 505 ILE cc_start: 0.8324 (pt) cc_final: 0.8118 (pt) REVERT: B 678 THR cc_start: 0.7906 (p) cc_final: 0.7517 (t) outliers start: 20 outliers final: 10 residues processed: 242 average time/residue: 0.2934 time to fit residues: 105.4914 Evaluate side-chains 182 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 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 183 SER Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 647 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 138 optimal weight: 0.0980 chunk 155 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 325 HIS B 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.174519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133072 restraints weight = 17783.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133668 restraints weight = 16829.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134566 restraints weight = 15064.097| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3389 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= 0.144 Angle : 0.574 8.827 18459 Z= 0.304 Chirality : 0.040 0.155 2163 Planarity : 0.004 0.038 2189 Dihedral : 15.262 89.201 2185 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.27 % Allowed : 10.32 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1564 helix: 0.22 (0.17), residues: 897 sheet: 1.07 (0.39), residues: 158 loop : 0.53 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.019 0.001 HIS B 284 PHE 0.016 0.001 PHE A 765 TYR 0.012 0.001 TYR A 228 ARG 0.004 0.000 ARG A 735 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 647) hydrogen bonds : angle 4.35146 ( 1870) covalent geometry : bond 0.00334 (13559) covalent geometry : angle 0.57377 (18459) *********************** 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 224 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7573 (p-90) cc_final: 0.7108 (p-90) REVERT: A 582 ILE cc_start: 0.8933 (mm) cc_final: 0.8673 (mt) REVERT: A 657 MET cc_start: 0.7388 (tpp) cc_final: 0.7107 (mpp) REVERT: A 660 ASP cc_start: 0.6795 (m-30) cc_final: 0.6407 (t0) REVERT: A 758 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: B 73 ASN cc_start: 0.7863 (m-40) cc_final: 0.7627 (m110) REVERT: B 126 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: B 169 ASP cc_start: 0.7221 (t0) cc_final: 0.6681 (m-30) REVERT: B 183 SER cc_start: 0.8202 (m) cc_final: 0.7814 (t) REVERT: B 355 ASP cc_start: 0.7520 (t0) cc_final: 0.7296 (t70) REVERT: B 484 LYS cc_start: 0.8162 (tptp) cc_final: 0.7924 (pttt) REVERT: B 505 ILE cc_start: 0.8291 (pt) cc_final: 0.8066 (pt) outliers start: 31 outliers final: 20 residues processed: 216 average time/residue: 0.3685 time to fit residues: 121.2540 Evaluate side-chains 194 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 61 optimal weight: 0.8980 chunk 148 optimal weight: 0.0370 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 270 ASN A 325 HIS B 888 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.175132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133697 restraints weight = 17549.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134701 restraints weight = 16433.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135182 restraints weight = 15583.230| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13559 Z= 0.129 Angle : 0.555 9.336 18459 Z= 0.290 Chirality : 0.039 0.132 2163 Planarity : 0.003 0.038 2189 Dihedral : 15.252 89.330 2185 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.27 % Allowed : 11.71 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1564 helix: 0.59 (0.17), residues: 887 sheet: 1.03 (0.40), residues: 155 loop : 0.61 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 661 HIS 0.006 0.001 HIS B 325 PHE 0.012 0.001 PHE B 765 TYR 0.015 0.001 TYR A 171 ARG 0.003 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 647) hydrogen bonds : angle 4.12359 ( 1870) covalent geometry : bond 0.00298 (13559) covalent geometry : angle 0.55455 (18459) *********************** 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 214 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7551 (p-90) cc_final: 0.7070 (p-90) REVERT: A 423 GLU cc_start: 0.7243 (tp30) cc_final: 0.6139 (pm20) REVERT: A 582 ILE cc_start: 0.8895 (mm) cc_final: 0.8654 (mt) REVERT: A 660 ASP cc_start: 0.6831 (m-30) cc_final: 0.6435 (t0) REVERT: A 758 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 768 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6461 (mtm-85) REVERT: B 126 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6457 (mp0) REVERT: B 169 ASP cc_start: 0.7293 (t0) cc_final: 0.6799 (m-30) REVERT: B 183 SER cc_start: 0.8217 (m) cc_final: 0.7807 (t) REVERT: B 316 MET cc_start: 0.6902 (ttm) cc_final: 0.6699 (ttp) REVERT: B 355 ASP cc_start: 0.7587 (t0) cc_final: 0.7333 (t70) REVERT: B 484 LYS cc_start: 0.8277 (tptp) cc_final: 0.7941 (pttt) REVERT: B 505 ILE cc_start: 0.8251 (pt) cc_final: 0.8000 (pt) outliers start: 31 outliers final: 22 residues processed: 205 average time/residue: 0.3394 time to fit residues: 102.7830 Evaluate side-chains 188 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 364 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR 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 17 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A 325 HIS B 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.176929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135199 restraints weight = 17634.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135616 restraints weight = 17394.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136559 restraints weight = 15232.907| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13559 Z= 0.112 Angle : 0.528 9.246 18459 Z= 0.276 Chirality : 0.038 0.132 2163 Planarity : 0.003 0.038 2189 Dihedral : 15.153 89.831 2185 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.42 % Allowed : 12.01 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1564 helix: 0.82 (0.18), residues: 892 sheet: 1.00 (0.39), residues: 158 loop : 0.51 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.005 0.001 HIS B 325 PHE 0.017 0.001 PHE A 415 TYR 0.009 0.001 TYR A 474 ARG 0.003 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 647) hydrogen bonds : angle 3.97211 ( 1870) covalent geometry : bond 0.00255 (13559) covalent geometry : angle 0.52778 (18459) *********************** 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 214 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7573 (p-90) cc_final: 0.7022 (p-90) REVERT: A 207 MET cc_start: 0.8857 (tpt) cc_final: 0.8231 (mmt) REVERT: A 423 GLU cc_start: 0.7131 (tp30) cc_final: 0.6075 (pm20) REVERT: A 582 ILE cc_start: 0.8904 (mm) cc_final: 0.8672 (mt) REVERT: A 660 ASP cc_start: 0.6818 (m-30) cc_final: 0.6445 (t0) REVERT: A 758 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: A 768 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.6496 (mtm-85) REVERT: B 126 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6348 (mp0) REVERT: B 169 ASP cc_start: 0.7267 (t0) cc_final: 0.6780 (m-30) REVERT: B 183 SER cc_start: 0.8190 (m) cc_final: 0.7760 (t) REVERT: B 284 HIS cc_start: 0.6739 (p90) cc_final: 0.6399 (p90) REVERT: B 355 ASP cc_start: 0.7568 (t0) cc_final: 0.7320 (t70) REVERT: B 484 LYS cc_start: 0.8262 (tptp) cc_final: 0.7914 (pttt) REVERT: B 505 ILE cc_start: 0.8269 (pt) cc_final: 0.8065 (pt) outliers start: 33 outliers final: 24 residues processed: 203 average time/residue: 0.2674 time to fit residues: 80.3979 Evaluate side-chains 189 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 421 THR 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 70 LEU 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 562 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 663 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 32 optimal weight: 0.0040 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 95 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- 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 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.178842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137831 restraints weight = 17785.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137624 restraints weight = 16606.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139003 restraints weight = 15823.983| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13559 Z= 0.101 Angle : 0.523 11.681 18459 Z= 0.272 Chirality : 0.038 0.132 2163 Planarity : 0.003 0.036 2189 Dihedral : 15.056 88.825 2185 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.90 % Allowed : 12.59 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1564 helix: 1.09 (0.18), residues: 879 sheet: 1.00 (0.39), residues: 160 loop : 0.54 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 HIS 0.005 0.001 HIS B 325 PHE 0.015 0.001 PHE A 415 TYR 0.015 0.001 TYR B 362 ARG 0.009 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 647) hydrogen bonds : angle 3.87801 ( 1870) covalent geometry : bond 0.00224 (13559) covalent geometry : angle 0.52305 (18459) *********************** 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 207 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7593 (p-90) cc_final: 0.7021 (p-90) REVERT: A 207 MET cc_start: 0.8749 (tpt) cc_final: 0.8102 (mmt) REVERT: A 295 SER cc_start: 0.8328 (p) cc_final: 0.7845 (m) REVERT: A 582 ILE cc_start: 0.8895 (mm) cc_final: 0.8676 (mt) REVERT: A 590 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 758 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7243 (m-80) REVERT: A 768 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.6890 (mtm-85) REVERT: A 825 ASN cc_start: 0.6870 (OUTLIER) cc_final: 0.6558 (t0) REVERT: B 126 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6303 (mp0) REVERT: B 169 ASP cc_start: 0.7199 (t0) cc_final: 0.6759 (m-30) REVERT: B 183 SER cc_start: 0.8136 (m) cc_final: 0.7774 (t) REVERT: B 284 HIS cc_start: 0.6671 (p90) cc_final: 0.6394 (p90) REVERT: B 355 ASP cc_start: 0.7535 (t0) cc_final: 0.7290 (t70) REVERT: B 484 LYS cc_start: 0.8196 (tptp) cc_final: 0.7887 (pttt) REVERT: B 505 ILE cc_start: 0.8219 (pt) cc_final: 0.7972 (pt) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.2378 time to fit residues: 69.3670 Evaluate side-chains 177 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 364 LEU 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 B residue 87 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 620 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.0050 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0770 chunk 99 optimal weight: 7.9990 chunk 111 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- 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 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.179692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138140 restraints weight = 17646.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138196 restraints weight = 17304.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139651 restraints weight = 14901.945| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4434 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= 0.100 Angle : 0.518 10.284 18459 Z= 0.268 Chirality : 0.037 0.130 2163 Planarity : 0.003 0.039 2189 Dihedral : 14.965 88.363 2185 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.98 % Allowed : 12.88 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1564 helix: 1.25 (0.18), residues: 878 sheet: 1.08 (0.40), residues: 156 loop : 0.58 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.005 0.001 HIS B 325 PHE 0.013 0.001 PHE B 670 TYR 0.011 0.001 TYR B 331 ARG 0.006 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 647) hydrogen bonds : angle 3.79361 ( 1870) covalent geometry : bond 0.00221 (13559) covalent geometry : angle 0.51793 (18459) *********************** 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 193 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.8759 (tpt) cc_final: 0.8129 (mmt) REVERT: A 295 SER cc_start: 0.8264 (p) cc_final: 0.7824 (m) REVERT: A 582 ILE cc_start: 0.8889 (mm) cc_final: 0.8675 (mt) REVERT: A 590 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 758 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: A 768 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.6866 (mtm-85) REVERT: A 825 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6525 (t0) REVERT: B 169 ASP cc_start: 0.7187 (t0) cc_final: 0.6748 (m-30) REVERT: B 183 SER cc_start: 0.8173 (m) cc_final: 0.7749 (t) REVERT: B 284 HIS cc_start: 0.6629 (p90) cc_final: 0.6343 (p90) REVERT: B 355 ASP cc_start: 0.7549 (t0) cc_final: 0.7307 (t70) REVERT: B 484 LYS cc_start: 0.8187 (tptp) cc_final: 0.7871 (pttt) REVERT: B 505 ILE cc_start: 0.8239 (pt) cc_final: 0.7986 (pt) REVERT: B 775 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8261 (tm-30) outliers start: 27 outliers final: 20 residues processed: 183 average time/residue: 0.2210 time to fit residues: 61.4621 Evaluate side-chains 182 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 590 LEU 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 102 LEU 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 620 SER Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0233 > 50: distance: 64 - 70: 27.809 distance: 70 - 71: 18.066 distance: 71 - 72: 46.454 distance: 71 - 74: 32.914 distance: 72 - 73: 6.533 distance: 74 - 75: 31.812 distance: 76 - 77: 7.920 distance: 77 - 78: 13.224 distance: 77 - 80: 32.095 distance: 78 - 79: 12.485 distance: 78 - 83: 21.736 distance: 79 - 109: 37.905 distance: 80 - 81: 17.737 distance: 80 - 82: 6.188 distance: 84 - 85: 17.664 distance: 85 - 86: 41.934 distance: 85 - 91: 33.923 distance: 86 - 116: 31.031 distance: 88 - 90: 28.596 distance: 91 - 92: 30.274 distance: 92 - 95: 3.473 distance: 93 - 100: 17.528 distance: 95 - 96: 32.778 distance: 96 - 97: 36.499 distance: 97 - 98: 37.990 distance: 97 - 99: 4.336 distance: 100 - 101: 8.131 distance: 101 - 102: 6.051 distance: 101 - 104: 36.556 distance: 102 - 109: 27.397 distance: 104 - 105: 14.824 distance: 105 - 106: 30.576 distance: 106 - 107: 14.660 distance: 107 - 108: 40.108 distance: 109 - 110: 30.219 distance: 110 - 111: 4.961 distance: 111 - 112: 4.269 distance: 111 - 116: 37.733 distance: 113 - 114: 45.402 distance: 116 - 117: 18.819 distance: 117 - 118: 30.076 distance: 117 - 120: 12.831 distance: 118 - 119: 15.149 distance: 118 - 123: 37.571 distance: 120 - 121: 27.570 distance: 120 - 122: 18.308 distance: 123 - 124: 7.196 distance: 123 - 129: 22.656 distance: 124 - 125: 15.536 distance: 124 - 127: 7.636 distance: 125 - 126: 29.345 distance: 125 - 130: 14.121 distance: 127 - 128: 18.201 distance: 128 - 129: 8.777 distance: 130 - 131: 31.266 distance: 131 - 132: 43.632 distance: 131 - 134: 25.745 distance: 132 - 133: 39.527 distance: 134 - 135: 20.459 distance: 135 - 136: 6.974 distance: 135 - 137: 14.606 distance: 136 - 138: 5.429 distance: 137 - 139: 21.529 distance: 137 - 140: 34.217 distance: 138 - 139: 6.514 distance: 139 - 141: 8.749 distance: 140 - 142: 11.333 distance: 141 - 143: 42.812 distance: 142 - 143: 11.938 distance: 145 - 146: 40.359 distance: 146 - 147: 30.562 distance: 146 - 148: 30.937