Starting phenix.real_space_refine on Fri Jul 3 08:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh9_44537/07_2026/9bh9_44537.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 49 5.49 5 S 78 5.16 5 C 8279 2.51 5 N 2221 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13155 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} 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: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} 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: "X" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 235 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3} Unresolved non-hydrogen planarities: 58 Chain: "Y" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 514 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1, ' DT:plan': 10, ' DG:plan': 6, ' DG:plan2': 6, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 5, ' DC:plan2': 5} Unresolved non-hydrogen planarities: 252 Time building chain proxies: 2.48, per 1000 atoms: 0.19 Number of scatterers: 13155 At special positions: 0 Unit cell: (124.95, 149.94, 91.63, 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 49 15.00 O 2528 8.00 N 2221 7.00 C 8279 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: 0.77 Conformation dependent library (CDL) restraints added in 509.5 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 60.5% alpha, 8.6% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.831A 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 removed outlier: 3.781A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 120 through 121 No H-bonds generated for 'chain 'A' and resid 120 through 121' Processing helix chain 'A' and resid 122 through 136 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 210 removed outlier: 3.519A pdb=" N LEU A 210 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.743A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.012A 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: 3.536A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.580A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.660A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) 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 478 removed outlier: 3.622A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.525A pdb=" N GLY A 482 " --> pdb=" O GLY A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 500 through 509 removed outlier: 4.035A pdb=" N GLY A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.851A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.510A 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 563 removed outlier: 3.865A pdb=" N ALA A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 removed outlier: 3.848A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 640 removed outlier: 4.336A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 677 through 686 removed outlier: 4.259A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.982A pdb=" N ALA A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.592A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.768A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 removed outlier: 4.324A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 798 through 802 removed outlier: 4.336A pdb=" N LEU A 801 " --> pdb=" O ARG A 798 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 802 " --> pdb=" O VAL A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 802' Processing helix chain 'A' and resid 803 through 812 removed outlier: 4.591A pdb=" N LEU A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.708A pdb=" N GLU A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 860 " --> pdb=" O ARG A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 891 removed outlier: 4.459A pdb=" N ALA A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.534A pdb=" N GLY B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' 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: 3.685A pdb=" N LEU B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 3.522A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.302A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 368 removed outlier: 3.527A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 389 " --> pdb=" O LYS B 385 " (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 removed outlier: 3.529A pdb=" N GLY B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.852A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.790A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.994A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 4.219A pdb=" N LEU B 653 " --> pdb=" O HIS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 677 through 688 removed outlier: 4.271A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 706 through 730 removed outlier: 4.381A pdb=" N ARG B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.899A pdb=" N GLN B 739 " --> pdb=" O ARG B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 770 removed outlier: 3.671A pdb=" N GLN B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 790 through 799 removed outlier: 4.141A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 813 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 825 through 835 Processing helix chain 'B' and resid 849 through 859 removed outlier: 3.674A pdb=" N VAL B 853 " --> pdb=" O GLU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 891 removed outlier: 5.086A pdb=" N ALA B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.737A 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: 7.106A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 111 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N SER A 265 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 113 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.995A pdb=" N ILE A 302 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.813A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.341A pdb=" N LYS B 139 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 213 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 141 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL B 215 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 143 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 260 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 111 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER B 265 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR B 113 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B 110 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR B 283 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 112 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.602A pdb=" N LEU B 309 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 304 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 340 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 442 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 342 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 414 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 621 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3879 1.33 - 1.45: 1835 1.45 - 1.57: 7510 1.57 - 1.69: 97 1.69 - 1.81: 124 Bond restraints: 13445 Sorted by residual: bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.65e+01 bond pdb=" C3' DA Y 40 " pdb=" C2' DA Y 40 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DC Y 52 " pdb=" C2' DC Y 52 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DT Y 39 " pdb=" C2' DT Y 39 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG Y 30 " pdb=" C2' DG Y 30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 13440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 17469 1.54 - 3.08: 707 3.08 - 4.62: 100 4.62 - 6.16: 17 6.16 - 7.70: 4 Bond angle restraints: 18297 Sorted by residual: angle pdb=" O5' DG X 50 " pdb=" C5' DG X 50 " pdb=" C4' DG X 50 " ideal model delta sigma weight residual 109.40 114.18 -4.78 8.00e-01 1.56e+00 3.56e+01 angle pdb=" O5' DA Y 37 " pdb=" C5' DA Y 37 " pdb=" C4' DA Y 37 " ideal model delta sigma weight residual 109.40 113.50 -4.10 8.00e-01 1.56e+00 2.63e+01 angle pdb=" O5' DT X 46 " pdb=" C5' DT X 46 " pdb=" C4' DT X 46 " ideal model delta sigma weight residual 109.40 113.44 -4.04 8.00e-01 1.56e+00 2.54e+01 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 110.10 105.34 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" O4' DG Y 30 " pdb=" C4' DG Y 30 " pdb=" C3' DG Y 30 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 ... (remaining 18292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 7849 31.28 - 62.57: 280 62.57 - 93.85: 18 93.85 - 125.13: 0 125.13 - 156.41: 1 Dihedral angle restraints: 8148 sinusoidal: 3588 harmonic: 4560 Sorted by residual: dihedral pdb=" CA ARG B 311 " pdb=" C ARG B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 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 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG A 521 " pdb=" C ARG A 521 " pdb=" N ARG A 522 " pdb=" CA ARG A 522 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 8145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1780 0.061 - 0.121: 329 0.121 - 0.182: 42 0.182 - 0.242: 0 0.242 - 0.303: 1 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C3' DT X 48 " pdb=" C4' DT X 48 " pdb=" O3' DT X 48 " pdb=" C2' DT X 48 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ARG A 768 " pdb=" N ARG A 768 " pdb=" C ARG A 768 " pdb=" CB ARG A 768 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" C3' DG Y 23 " pdb=" C4' DG Y 23 " pdb=" O3' DG Y 23 " pdb=" C2' DG Y 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2149 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT X 49 " -0.036 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT X 49 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DT X 49 " -0.027 2.00e-02 2.50e+03 pdb=" O2 DT X 49 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT X 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT X 49 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT X 49 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT X 49 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT X 49 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT X 49 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 38 " 0.008 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" N9 DG Y 38 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG Y 38 " 0.044 2.00e-02 2.50e+03 pdb=" N7 DG Y 38 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG Y 38 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG Y 38 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG Y 38 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG Y 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG Y 38 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG Y 38 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG Y 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG Y 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 843 " -0.241 9.50e-02 1.11e+02 1.09e-01 8.88e+00 pdb=" NE ARG B 843 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 843 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 843 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 843 " -0.001 2.00e-02 2.50e+03 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4365 2.87 - 3.38: 12628 3.38 - 3.88: 20465 3.88 - 4.39: 24606 4.39 - 4.90: 40811 Nonbonded interactions: 102875 Sorted by model distance: nonbonded pdb=" OE1 GLU A 792 " pdb=" OH TYR A 811 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OG SER A 722 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 782 " pdb=" N2 DG Y 42 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS B 352 " pdb=" OP2 DG Y 25 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP B 647 " pdb=" NH1 ARG B 784 " model vdw 2.394 3.120 ... (remaining 102870 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' selection = chain 'B' } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.004 0.034 13445 Z= 0.262 Angle : 0.711 7.696 18297 Z= 0.479 Chirality : 0.048 0.303 2152 Planarity : 0.009 0.109 2165 Dihedral : 15.034 156.414 5188 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.19), residues: 1550 helix: -2.44 (0.13), residues: 832 sheet: 0.41 (0.44), residues: 120 loop : 0.21 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG B 711 TYR 0.029 0.005 TYR A 239 PHE 0.019 0.001 PHE A 658 TRP 0.023 0.002 TRP B 666 HIS 0.011 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.26 (13445) covalent geometry : angle 0.71094 / 0.48 (18297) hydrogen bonds : bond 0.19775 / 12.90 ( 619) hydrogen bonds : angle 8.05052 / 5.80 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8395 (mp) cc_final: 0.7812 (tp) REVERT: A 391 MET cc_start: 0.6625 (ttp) cc_final: 0.5895 (ttm) REVERT: B 463 ILE cc_start: 0.8574 (mm) cc_final: 0.8289 (mt) REVERT: B 550 MET cc_start: 0.7723 (mtt) cc_final: 0.7466 (mtp) REVERT: B 645 GLU cc_start: 0.6617 (pt0) cc_final: 0.5937 (tt0) REVERT: B 782 GLN cc_start: 0.7295 (tt0) cc_final: 0.7065 (tt0) REVERT: B 784 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7662 (ttm110) outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.1365 time to fit residues: 57.7257 Evaluate side-chains 190 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 366 HIS A 416 HIS A 710 HIS B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 416 HIS B 434 GLN B 548 GLN B 709 GLN B 739 GLN B 780 GLN B 888 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.184088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140584 restraints weight = 16733.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136806 restraints weight = 22931.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138306 restraints weight = 22846.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138690 restraints weight = 16364.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138935 restraints weight = 15733.891| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13445 Z= 0.188 Angle : 0.713 10.215 18297 Z= 0.381 Chirality : 0.044 0.231 2152 Planarity : 0.005 0.047 2165 Dihedral : 15.140 164.085 2180 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.77 % Allowed : 6.64 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1550 helix: -0.93 (0.16), residues: 844 sheet: 0.47 (0.41), residues: 142 loop : 0.63 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 522 TYR 0.024 0.002 TYR A 331 PHE 0.018 0.002 PHE B 658 TRP 0.021 0.002 TRP A 661 HIS 0.007 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (13445) covalent geometry : angle 0.71323 / 0.38 (18297) hydrogen bonds : bond 0.05240 / 3.46 ( 619) hydrogen bonds : angle 5.24473 / 3.69 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8277 (mp) cc_final: 0.7794 (tp) outliers start: 24 outliers final: 14 residues processed: 219 average time/residue: 0.1268 time to fit residues: 39.0682 Evaluate side-chains 191 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.181085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136420 restraints weight = 16399.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135207 restraints weight = 17579.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135870 restraints weight = 17673.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136644 restraints weight = 14768.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136906 restraints weight = 13495.741| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13445 Z= 0.144 Angle : 0.636 9.626 18297 Z= 0.335 Chirality : 0.041 0.233 2152 Planarity : 0.004 0.045 2165 Dihedral : 15.112 164.539 2180 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.99 % Allowed : 9.29 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1550 helix: -0.35 (0.17), residues: 854 sheet: 0.52 (0.40), residues: 142 loop : 0.52 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 467 TYR 0.014 0.001 TYR A 171 PHE 0.029 0.002 PHE A 87 TRP 0.015 0.001 TRP A 661 HIS 0.009 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13445) covalent geometry : angle 0.63628 / 0.34 (18297) hydrogen bonds : bond 0.04352 / 2.88 ( 619) hydrogen bonds : angle 4.82711 / 3.37 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8269 (mp) cc_final: 0.7726 (tp) REVERT: A 391 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6040 (mtm) REVERT: A 655 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8560 (m) REVERT: B 325 HIS cc_start: 0.7414 (m90) cc_final: 0.7188 (m90) REVERT: B 784 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7973 (ttm-80) outliers start: 27 outliers final: 14 residues processed: 200 average time/residue: 0.1188 time to fit residues: 33.5838 Evaluate side-chains 177 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 30.0000 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.184555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146914 restraints weight = 16582.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145980 restraints weight = 20554.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144195 restraints weight = 22344.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142851 restraints weight = 20592.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143819 restraints weight = 18299.126| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13445 Z= 0.152 Angle : 0.600 8.170 18297 Z= 0.319 Chirality : 0.041 0.241 2152 Planarity : 0.004 0.044 2165 Dihedral : 15.152 164.442 2180 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.77 % Allowed : 10.32 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1550 helix: -0.02 (0.17), residues: 852 sheet: 0.56 (0.41), residues: 142 loop : 0.42 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 808 TYR 0.017 0.002 TYR B 811 PHE 0.056 0.002 PHE A 87 TRP 0.012 0.001 TRP B 666 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13445) covalent geometry : angle 0.59977 / 0.32 (18297) hydrogen bonds : bond 0.03993 / 2.64 ( 619) hydrogen bonds : angle 4.65666 / 3.24 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8130 (mp) cc_final: 0.7799 (tp) REVERT: A 655 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8575 (m) REVERT: B 216 ASP cc_start: 0.7238 (t0) cc_final: 0.7009 (t0) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.1142 time to fit residues: 29.9116 Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 311 ARG Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4103 r_free = 0.4103 target = 0.178727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133530 restraints weight = 16446.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131615 restraints weight = 18638.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132406 restraints weight = 19489.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132963 restraints weight = 15626.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133002 restraints weight = 14091.915| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13445 Z= 0.192 Angle : 0.626 12.170 18297 Z= 0.326 Chirality : 0.042 0.253 2152 Planarity : 0.004 0.045 2165 Dihedral : 15.100 164.068 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.36 % Allowed : 12.17 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1550 helix: 0.03 (0.17), residues: 848 sheet: 0.48 (0.42), residues: 142 loop : 0.36 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 522 TYR 0.013 0.002 TYR A 171 PHE 0.020 0.002 PHE A 765 TRP 0.012 0.001 TRP B 666 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13445) covalent geometry : angle 0.62573 / 0.33 (18297) hydrogen bonds : bond 0.04069 / 2.71 ( 619) hydrogen bonds : angle 4.63261 / 3.23 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8281 (mp) cc_final: 0.7782 (tp) REVERT: A 655 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8527 (m) REVERT: B 100 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7693 (mp) REVERT: B 216 ASP cc_start: 0.7522 (t0) cc_final: 0.7293 (t0) outliers start: 32 outliers final: 20 residues processed: 177 average time/residue: 0.1173 time to fit residues: 29.8090 Evaluate side-chains 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 37 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4130 r_free = 0.4130 target = 0.181367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134815 restraints weight = 16209.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134645 restraints weight = 18533.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135755 restraints weight = 16815.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136039 restraints weight = 13529.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136399 restraints weight = 13206.073| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13445 Z= 0.123 Angle : 0.590 10.735 18297 Z= 0.306 Chirality : 0.040 0.230 2152 Planarity : 0.004 0.042 2165 Dihedral : 15.004 164.513 2178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.99 % Allowed : 12.91 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1550 helix: 0.31 (0.18), residues: 856 sheet: 0.57 (0.41), residues: 142 loop : 0.28 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.021 0.001 TYR A 811 PHE 0.016 0.001 PHE B 181 TRP 0.013 0.001 TRP A 661 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13445) covalent geometry : angle 0.58996 / 0.31 (18297) hydrogen bonds : bond 0.03640 / 2.41 ( 619) hydrogen bonds : angle 4.42048 / 3.06 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8205 (mp) cc_final: 0.7705 (tp) REVERT: A 478 VAL cc_start: 0.8212 (m) cc_final: 0.8006 (t) REVERT: A 655 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8524 (m) REVERT: A 776 LEU cc_start: 0.7456 (mt) cc_final: 0.7216 (mt) REVERT: B 100 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7618 (mp) REVERT: B 101 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 197 LEU cc_start: 0.8898 (tp) cc_final: 0.8655 (tt) outliers start: 27 outliers final: 14 residues processed: 184 average time/residue: 0.1215 time to fit residues: 32.0003 Evaluate side-chains 174 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 0.3980 chunk 2 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4147 r_free = 0.4147 target = 0.181983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137777 restraints weight = 16639.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135423 restraints weight = 22244.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136734 restraints weight = 22039.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137066 restraints weight = 17165.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137146 restraints weight = 15797.456| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13445 Z= 0.150 Angle : 0.606 12.410 18297 Z= 0.312 Chirality : 0.041 0.240 2152 Planarity : 0.004 0.040 2165 Dihedral : 14.995 164.146 2178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.70 % Allowed : 14.53 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1550 helix: 0.40 (0.18), residues: 850 sheet: 0.51 (0.42), residues: 142 loop : 0.18 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 705 TYR 0.013 0.001 TYR A 331 PHE 0.047 0.002 PHE A 87 TRP 0.009 0.001 TRP A 661 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13445) covalent geometry : angle 0.60616 / 0.31 (18297) hydrogen bonds : bond 0.03685 / 2.44 ( 619) hydrogen bonds : angle 4.39074 / 3.04 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 293 LEU cc_start: 0.8195 (mp) cc_final: 0.7770 (tp) REVERT: A 655 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8529 (m) REVERT: B 100 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7623 (mp) REVERT: B 101 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 197 LEU cc_start: 0.8896 (tp) cc_final: 0.8682 (tt) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 0.1135 time to fit residues: 28.6414 Evaluate side-chains 173 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 119 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.182011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136627 restraints weight = 16048.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135311 restraints weight = 18950.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136094 restraints weight = 19103.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136670 restraints weight = 15655.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136658 restraints weight = 14403.767| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13445 Z= 0.113 Angle : 0.600 11.951 18297 Z= 0.310 Chirality : 0.040 0.221 2152 Planarity : 0.004 0.072 2165 Dihedral : 14.965 164.624 2178 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.77 % Allowed : 14.16 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1550 helix: 0.57 (0.18), residues: 856 sheet: 0.58 (0.41), residues: 146 loop : 0.20 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 884 TYR 0.013 0.001 TYR A 331 PHE 0.015 0.001 PHE B 93 TRP 0.019 0.001 TRP A 666 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13445) covalent geometry : angle 0.60005 / 0.31 (18297) hydrogen bonds : bond 0.03379 / 2.20 ( 619) hydrogen bonds : angle 4.28488 / 2.95 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 293 LEU cc_start: 0.8208 (mp) cc_final: 0.7740 (tp) REVERT: A 640 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6378 (pttt) REVERT: A 655 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8470 (m) REVERT: B 100 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 101 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (mm) REVERT: B 197 LEU cc_start: 0.8892 (tp) cc_final: 0.8676 (tt) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 0.1248 time to fit residues: 32.9358 Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 96 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.184405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144229 restraints weight = 16656.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143036 restraints weight = 27570.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144081 restraints weight = 28119.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143728 restraints weight = 20686.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144143 restraints weight = 18837.188| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13445 Z= 0.174 Angle : 0.635 11.465 18297 Z= 0.327 Chirality : 0.042 0.244 2152 Planarity : 0.004 0.050 2165 Dihedral : 14.974 164.360 2178 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.47 % Allowed : 15.19 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1550 helix: 0.43 (0.18), residues: 850 sheet: 0.56 (0.42), residues: 146 loop : 0.19 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 705 TYR 0.012 0.002 TYR A 331 PHE 0.020 0.002 PHE A 765 TRP 0.048 0.002 TRP A 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (13445) covalent geometry : angle 0.63526 / 0.33 (18297) hydrogen bonds : bond 0.03660 / 2.43 ( 619) hydrogen bonds : angle 4.33724 / 3.02 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 293 LEU cc_start: 0.8123 (mp) cc_final: 0.7861 (tp) REVERT: A 640 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6640 (pttt) REVERT: A 655 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 100 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7797 (mp) REVERT: B 101 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7978 (mm) outliers start: 20 outliers final: 13 residues processed: 171 average time/residue: 0.1252 time to fit residues: 30.6038 Evaluate side-chains 177 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 150 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 GLN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.186299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144250 restraints weight = 16441.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141722 restraints weight = 24115.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142975 restraints weight = 23439.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143106 restraints weight = 17180.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143440 restraints weight = 16732.256| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13445 Z= 0.118 Angle : 0.612 11.393 18297 Z= 0.314 Chirality : 0.040 0.219 2152 Planarity : 0.004 0.049 2165 Dihedral : 14.955 165.040 2178 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.55 % Allowed : 15.49 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1550 helix: 0.58 (0.18), residues: 856 sheet: 0.56 (0.42), residues: 146 loop : 0.23 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 705 TYR 0.012 0.001 TYR A 331 PHE 0.013 0.001 PHE B 181 TRP 0.043 0.002 TRP A 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13445) covalent geometry : angle 0.61206 / 0.31 (18297) hydrogen bonds : bond 0.03312 / 2.18 ( 619) hydrogen bonds : angle 4.21708 / 2.92 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 293 LEU cc_start: 0.8073 (mp) cc_final: 0.7763 (tp) REVERT: A 640 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6457 (pttt) REVERT: A 655 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8457 (m) REVERT: B 100 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 101 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7976 (mm) outliers start: 21 outliers final: 13 residues processed: 180 average time/residue: 0.1343 time to fit residues: 34.2446 Evaluate side-chains 178 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139517 restraints weight = 16507.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137767 restraints weight = 23367.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139034 restraints weight = 20590.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139196 restraints weight = 17589.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141302 restraints weight = 15199.437| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 13445 Z= 0.192 Angle : 0.839 59.200 18297 Z= 0.471 Chirality : 0.041 0.265 2152 Planarity : 0.004 0.050 2165 Dihedral : 14.953 165.020 2178 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.25 % Allowed : 15.78 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1550 helix: 0.58 (0.18), residues: 856 sheet: 0.55 (0.42), residues: 146 loop : 0.22 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 705 TYR 0.012 0.001 TYR A 331 PHE 0.014 0.001 PHE A 464 TRP 0.038 0.001 TRP A 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (13445) covalent geometry : angle 0.83946 / 0.47 (18297) hydrogen bonds : bond 0.03323 / 2.19 ( 619) hydrogen bonds : angle 4.21560 / 2.92 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.04 seconds wall clock time: 34 minutes 9.80 seconds (2049.80 seconds total)