Starting phenix.real_space_refine on Mon Aug 5 10:35:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_44538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_44538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_44538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_44538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bha_44538/08_2024/9bha_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 Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.14, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 5.30 Conformation dependent library (CDL) restraints added in 2.2 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: 4.04 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: 4.87 Time building geometry restraints manager: 5.78 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: 98.73 - 105.80: 424 105.80 - 112.87: 7431 112.87 - 119.93: 4754 119.93 - 127.00: 5660 127.00 - 134.07: 190 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: 3.270 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.890 ------------------------------------------------------------------------------- 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= 0.178 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.576 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: 0.3061 time to fit residues: 133.6122 Evaluate side-chains 174 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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= 0.185 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7539 (p-90) cc_final: 0.7085 (p-90) REVERT: A 423 GLU cc_start: 0.7201 (tp30) cc_final: 0.6090 (pm20) REVERT: A 634 ASP cc_start: 0.6681 (m-30) cc_final: 0.6451 (m-30) REVERT: A 660 ASP cc_start: 0.6828 (m-30) cc_final: 0.6343 (t0) REVERT: A 758 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: B 70 LEU cc_start: 0.8231 (tp) cc_final: 0.7593 (tt) REVERT: B 73 ASN cc_start: 0.7843 (m-40) cc_final: 0.7411 (m110) REVERT: B 87 PHE cc_start: 0.7613 (m-80) cc_final: 0.7387 (m-10) REVERT: B 126 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: B 169 ASP cc_start: 0.7182 (t0) cc_final: 0.6658 (m-30) REVERT: B 183 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7777 (t) REVERT: B 505 ILE cc_start: 0.8268 (pt) cc_final: 0.8057 (pt) REVERT: B 678 THR cc_start: 0.7914 (p) cc_final: 0.7520 (t) outliers start: 20 outliers final: 10 residues processed: 242 average time/residue: 0.2641 time to fit residues: 93.3853 Evaluate side-chains 182 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 81 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13559 Z= 0.200 Angle : 0.565 8.646 18459 Z= 0.299 Chirality : 0.040 0.150 2163 Planarity : 0.004 0.038 2189 Dihedral : 15.240 89.894 2185 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.20 % Allowed : 10.54 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.21), residues: 1564 helix: 0.25 (0.17), residues: 899 sheet: 1.11 (0.39), residues: 158 loop : 0.56 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 74 HIS 0.018 0.001 HIS B 284 PHE 0.014 0.001 PHE A 765 TYR 0.013 0.001 TYR B 283 ARG 0.004 0.000 ARG A 735 *********************** 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 222 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7558 (p-90) cc_final: 0.7096 (p-90) REVERT: A 582 ILE cc_start: 0.8930 (mm) cc_final: 0.8650 (mt) REVERT: A 634 ASP cc_start: 0.6834 (m-30) cc_final: 0.6620 (m-30) REVERT: A 657 MET cc_start: 0.7372 (tpp) cc_final: 0.7089 (mpp) REVERT: A 660 ASP cc_start: 0.6840 (m-30) cc_final: 0.6384 (t0) REVERT: A 758 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: B 73 ASN cc_start: 0.7919 (m-40) cc_final: 0.7676 (m110) REVERT: B 126 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: B 169 ASP cc_start: 0.7196 (t0) cc_final: 0.6657 (m-30) REVERT: B 183 SER cc_start: 0.8132 (m) cc_final: 0.7743 (t) REVERT: B 484 LYS cc_start: 0.8121 (tptp) cc_final: 0.7906 (pttt) REVERT: B 505 ILE cc_start: 0.8225 (pt) cc_final: 0.7986 (pt) outliers start: 30 outliers final: 20 residues processed: 214 average time/residue: 0.2424 time to fit residues: 76.2533 Evaluate side-chains 195 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 145 optimal weight: 0.9980 chunk 110 optimal weight: 0.0270 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 284 HIS B 888 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3778 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= 0.168 Angle : 0.537 9.550 18459 Z= 0.282 Chirality : 0.039 0.132 2163 Planarity : 0.003 0.037 2189 Dihedral : 15.206 89.549 2185 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.20 % Allowed : 11.93 % Favored : 85.87 % 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: 0.89 (0.21), residues: 1564 helix: 0.64 (0.17), residues: 893 sheet: 1.17 (0.39), residues: 153 loop : 0.62 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 661 HIS 0.013 0.001 HIS B 284 PHE 0.012 0.001 PHE B 765 TYR 0.013 0.001 TYR A 474 ARG 0.003 0.000 ARG A 823 *********************** 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 219 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7535 (p-90) cc_final: 0.7074 (p-90) REVERT: A 207 MET cc_start: 0.8862 (tpt) cc_final: 0.8242 (mmt) REVERT: A 423 GLU cc_start: 0.7090 (tp30) cc_final: 0.6100 (pm20) REVERT: A 582 ILE cc_start: 0.8914 (mm) cc_final: 0.8656 (mt) REVERT: A 660 ASP cc_start: 0.6861 (m-30) cc_final: 0.6451 (t0) REVERT: A 758 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: A 768 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.6733 (mtm-85) REVERT: A 856 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7199 (ptp-110) REVERT: B 126 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6477 (mp0) REVERT: B 169 ASP cc_start: 0.7189 (t0) cc_final: 0.6699 (m-30) REVERT: B 183 SER cc_start: 0.8152 (m) cc_final: 0.7757 (t) REVERT: B 484 LYS cc_start: 0.8204 (tptp) cc_final: 0.7916 (pttt) REVERT: B 505 ILE cc_start: 0.8185 (pt) cc_final: 0.7964 (pt) outliers start: 30 outliers final: 20 residues processed: 210 average time/residue: 0.2504 time to fit residues: 77.1061 Evaluate side-chains 183 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE 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 329 LEU Chi-restraints excluded: chain A residue 364 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 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 130 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13559 Z= 0.236 Angle : 0.568 9.373 18459 Z= 0.297 Chirality : 0.040 0.133 2163 Planarity : 0.004 0.039 2189 Dihedral : 15.243 87.415 2185 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.78 % Allowed : 12.01 % Favored : 85.21 % 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: 0.79 (0.21), residues: 1564 helix: 0.66 (0.17), residues: 890 sheet: 1.00 (0.39), residues: 158 loop : 0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 666 HIS 0.007 0.001 HIS B 325 PHE 0.016 0.001 PHE A 415 TYR 0.013 0.001 TYR A 228 ARG 0.003 0.000 ARG B 137 *********************** 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 215 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7620 (p-90) cc_final: 0.7084 (p-90) REVERT: A 207 MET cc_start: 0.8899 (tpt) cc_final: 0.8219 (mmt) REVERT: A 295 SER cc_start: 0.8297 (p) cc_final: 0.7887 (m) REVERT: A 582 ILE cc_start: 0.8929 (mm) cc_final: 0.8689 (mt) REVERT: A 657 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7159 (mpp) REVERT: A 660 ASP cc_start: 0.6819 (m-30) cc_final: 0.6539 (t0) REVERT: A 758 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 768 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.6687 (mtm-85) REVERT: B 126 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6400 (mp0) REVERT: B 169 ASP cc_start: 0.7235 (t0) cc_final: 0.6770 (m-30) REVERT: B 183 SER cc_start: 0.8128 (m) cc_final: 0.7719 (t) REVERT: B 284 HIS cc_start: 0.6834 (p90) cc_final: 0.6524 (p90) REVERT: B 484 LYS cc_start: 0.8239 (tptp) cc_final: 0.7908 (pttt) REVERT: B 505 ILE cc_start: 0.8155 (pt) cc_final: 0.7898 (pt) outliers start: 38 outliers final: 28 residues processed: 204 average time/residue: 0.2531 time to fit residues: 75.4316 Evaluate side-chains 197 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE 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 492 SER Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 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 209 LEU Chi-restraints excluded: chain B residue 333 THR 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 52 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 156 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13559 Z= 0.285 Angle : 0.611 10.936 18459 Z= 0.314 Chirality : 0.041 0.140 2163 Planarity : 0.004 0.042 2189 Dihedral : 15.295 86.371 2185 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.56 % Allowed : 12.74 % Favored : 84.70 % 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: 0.61 (0.21), residues: 1564 helix: 0.55 (0.17), residues: 888 sheet: 0.70 (0.41), residues: 156 loop : 0.33 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 666 HIS 0.007 0.001 HIS B 325 PHE 0.017 0.001 PHE A 765 TYR 0.014 0.002 TYR B 362 ARG 0.003 0.000 ARG B 137 *********************** 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 214 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.8931 (tpt) cc_final: 0.8177 (mmt) REVERT: A 295 SER cc_start: 0.8312 (p) cc_final: 0.7917 (m) REVERT: A 582 ILE cc_start: 0.8949 (mm) cc_final: 0.8721 (mt) REVERT: A 590 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 657 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7222 (mpp) REVERT: A 660 ASP cc_start: 0.6779 (m-30) cc_final: 0.6544 (t0) REVERT: A 758 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: A 768 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.6691 (mtm-85) REVERT: B 126 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6386 (mp0) REVERT: B 169 ASP cc_start: 0.7121 (t0) cc_final: 0.6707 (m-30) REVERT: B 183 SER cc_start: 0.8140 (m) cc_final: 0.7709 (t) REVERT: B 284 HIS cc_start: 0.6943 (p90) cc_final: 0.6633 (p90) REVERT: B 484 LYS cc_start: 0.8162 (tptp) cc_final: 0.7852 (pttt) REVERT: B 505 ILE cc_start: 0.8165 (pt) cc_final: 0.7902 (pt) REVERT: B 753 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6843 (mm-40) outliers start: 35 outliers final: 27 residues processed: 202 average time/residue: 0.2625 time to fit residues: 76.6350 Evaluate side-chains 198 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 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 333 THR Chi-restraints excluded: chain B residue 353 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 279 ASN ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13559 Z= 0.204 Angle : 0.566 10.296 18459 Z= 0.293 Chirality : 0.039 0.153 2163 Planarity : 0.004 0.040 2189 Dihedral : 15.189 88.706 2185 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 13.47 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.21), residues: 1564 helix: 0.72 (0.18), residues: 890 sheet: 0.77 (0.41), residues: 154 loop : 0.29 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 PHE 0.013 0.001 PHE B 765 TYR 0.014 0.001 TYR A 171 ARG 0.004 0.000 ARG B 137 *********************** 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 207 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.8956 (tpt) cc_final: 0.8263 (mmt) REVERT: A 295 SER cc_start: 0.8311 (p) cc_final: 0.7923 (m) REVERT: A 423 GLU cc_start: 0.7152 (tp30) cc_final: 0.6087 (pm20) REVERT: A 582 ILE cc_start: 0.8925 (mm) cc_final: 0.8697 (mt) REVERT: A 590 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 758 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: A 768 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.6733 (mtm-85) REVERT: B 126 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6404 (mp0) REVERT: B 169 ASP cc_start: 0.7248 (t0) cc_final: 0.6819 (m-30) REVERT: B 183 SER cc_start: 0.8145 (m) cc_final: 0.7749 (t) REVERT: B 284 HIS cc_start: 0.6895 (p90) cc_final: 0.6571 (p90) REVERT: B 484 LYS cc_start: 0.8139 (tptp) cc_final: 0.7867 (pttt) REVERT: B 505 ILE cc_start: 0.8175 (pt) cc_final: 0.7907 (pt) outliers start: 37 outliers final: 26 residues processed: 196 average time/residue: 0.2405 time to fit residues: 69.7065 Evaluate side-chains 183 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 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 333 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 337 ASN B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4419 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= 0.175 Angle : 0.546 10.780 18459 Z= 0.284 Chirality : 0.038 0.151 2163 Planarity : 0.003 0.038 2189 Dihedral : 15.163 89.845 2185 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.49 % Allowed : 14.49 % 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 (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: 0.88 (0.21), residues: 1564 helix: 0.87 (0.18), residues: 887 sheet: 0.75 (0.40), residues: 154 loop : 0.28 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 PHE 0.013 0.001 PHE B 765 TYR 0.016 0.001 TYR B 331 ARG 0.003 0.000 ARG B 456 *********************** 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 199 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7624 (p-90) cc_final: 0.7164 (p-90) REVERT: A 207 MET cc_start: 0.8904 (tpt) cc_final: 0.8248 (mmt) REVERT: A 295 SER cc_start: 0.8265 (p) cc_final: 0.7872 (m) REVERT: A 423 GLU cc_start: 0.7078 (tp30) cc_final: 0.6046 (pm20) REVERT: A 582 ILE cc_start: 0.8915 (mm) cc_final: 0.8700 (mt) REVERT: A 590 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 657 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7089 (mtm) REVERT: A 758 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: A 768 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.6844 (mtm-85) REVERT: B 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6822 (m-30) REVERT: B 183 SER cc_start: 0.8146 (m) cc_final: 0.7733 (t) REVERT: B 284 HIS cc_start: 0.6819 (p90) cc_final: 0.6499 (p90) REVERT: B 484 LYS cc_start: 0.8114 (tptp) cc_final: 0.7816 (pttt) REVERT: B 505 ILE cc_start: 0.8139 (pt) cc_final: 0.7889 (pt) REVERT: B 699 LYS cc_start: 0.7242 (ttmm) cc_final: 0.7034 (ttmm) REVERT: B 775 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8480 (tm-30) outliers start: 34 outliers final: 25 residues processed: 186 average time/residue: 0.2417 time to fit residues: 66.5606 Evaluate side-chains 186 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4513 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= 0.187 Angle : 0.554 10.997 18459 Z= 0.287 Chirality : 0.039 0.178 2163 Planarity : 0.003 0.038 2189 Dihedral : 15.150 89.873 2185 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.34 % Allowed : 14.28 % Favored : 83.38 % 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: 0.90 (0.22), residues: 1564 helix: 0.90 (0.18), residues: 888 sheet: 0.73 (0.40), residues: 154 loop : 0.26 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 PHE 0.013 0.001 PHE B 765 TYR 0.013 0.001 TYR A 331 ARG 0.004 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7636 (p-90) cc_final: 0.7145 (p-90) REVERT: A 207 MET cc_start: 0.8915 (tpt) cc_final: 0.8244 (mmt) REVERT: A 295 SER cc_start: 0.8228 (p) cc_final: 0.7831 (m) REVERT: A 423 GLU cc_start: 0.7054 (tp30) cc_final: 0.6050 (pm20) REVERT: A 582 ILE cc_start: 0.8926 (mm) cc_final: 0.8710 (mt) REVERT: A 590 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (mp) REVERT: A 657 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7160 (mtm) REVERT: A 758 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: A 768 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.6862 (mtm-85) REVERT: B 169 ASP cc_start: 0.7227 (t0) cc_final: 0.6789 (m-30) REVERT: B 183 SER cc_start: 0.8134 (m) cc_final: 0.7707 (t) REVERT: B 284 HIS cc_start: 0.6882 (p90) cc_final: 0.6543 (p90) REVERT: B 484 LYS cc_start: 0.8069 (tptp) cc_final: 0.7809 (pttt) REVERT: B 505 ILE cc_start: 0.8138 (pt) cc_final: 0.7886 (pt) REVERT: B 699 LYS cc_start: 0.7269 (ttmm) cc_final: 0.7059 (ttmm) outliers start: 32 outliers final: 26 residues processed: 183 average time/residue: 0.2369 time to fit residues: 64.3030 Evaluate side-chains 184 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 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 364 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 530 SER 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 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 153 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 0.0030 chunk 128 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 0.2968 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13559 Z= 0.150 Angle : 0.549 11.171 18459 Z= 0.284 Chirality : 0.038 0.162 2163 Planarity : 0.003 0.043 2189 Dihedral : 15.027 86.653 2185 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.46 % Allowed : 15.37 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.22), residues: 1564 helix: 1.09 (0.18), residues: 880 sheet: 0.75 (0.40), residues: 156 loop : 0.34 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 661 HIS 0.004 0.000 HIS B 325 PHE 0.012 0.001 PHE B 765 TYR 0.016 0.001 TYR B 362 ARG 0.010 0.000 ARG B 137 ********************** 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 198 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7629 (p-90) cc_final: 0.7152 (p-90) REVERT: A 207 MET cc_start: 0.8831 (tpt) cc_final: 0.8230 (mmt) REVERT: A 295 SER cc_start: 0.8162 (p) cc_final: 0.7762 (m) REVERT: A 582 ILE cc_start: 0.8912 (mm) cc_final: 0.8688 (mt) REVERT: A 657 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7205 (mtm) REVERT: A 758 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: A 768 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7000 (mtm-85) REVERT: A 825 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6537 (t0) REVERT: B 137 ARG cc_start: 0.7058 (mmp80) cc_final: 0.6499 (mmp-170) REVERT: B 169 ASP cc_start: 0.7189 (t0) cc_final: 0.6817 (m-30) REVERT: B 183 SER cc_start: 0.8120 (m) cc_final: 0.7675 (t) REVERT: B 284 HIS cc_start: 0.6844 (p90) cc_final: 0.6479 (p90) REVERT: B 484 LYS cc_start: 0.8052 (tptp) cc_final: 0.7740 (pttt) REVERT: B 505 ILE cc_start: 0.8106 (pt) cc_final: 0.7844 (pt) REVERT: B 699 LYS cc_start: 0.7062 (ttmm) cc_final: 0.6860 (ttmm) REVERT: B 775 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 20 outliers final: 13 residues processed: 189 average time/residue: 0.2628 time to fit residues: 71.4473 Evaluate side-chains 182 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 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 620 SER Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 744 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.175759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134891 restraints weight = 17632.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135235 restraints weight = 17084.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136126 restraints weight = 15605.674| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4738 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= 0.193 Angle : 0.570 11.268 18459 Z= 0.294 Chirality : 0.039 0.160 2163 Planarity : 0.004 0.046 2189 Dihedral : 15.083 89.133 2185 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.54 % Allowed : 15.45 % 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 (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: 1.05 (0.22), residues: 1564 helix: 1.01 (0.18), residues: 880 sheet: 0.85 (0.41), residues: 154 loop : 0.35 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 666 HIS 0.005 0.001 HIS A 716 PHE 0.012 0.001 PHE B 765 TYR 0.021 0.001 TYR B 331 ARG 0.010 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.83 seconds wall clock time: 47 minutes 31.81 seconds (2851.81 seconds total)