Starting phenix.real_space_refine on Sat Aug 23 15:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh9_44537/08_2025/9bh9_44537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh9_44537/08_2025/9bh9_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_44537/08_2025/9bh9_44537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh9_44537/08_2025/9bh9_44537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bh9_44537/08_2025/9bh9_44537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh9_44537/08_2025/9bh9_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-2.0-5787/lib/python3.9/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: 3.77, per 1000 atoms: 0.29 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: 1.21 Conformation dependent library (CDL) restraints added in 630.2 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 1.87 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: 2.69 Time building geometry restraints manager: 1.62 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=" C4' DT Y 39 " pdb=" O4' DT Y 39 " ideal model delta sigma weight residual 1.450 1.420 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C4' DA Y 40 " pdb=" O4' DA Y 40 " ideal model delta sigma weight residual 1.450 1.422 0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C2' DT X 48 " pdb=" C1' DT X 48 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C4' DT Y 22 " pdb=" O4' DT Y 22 " ideal model delta sigma weight residual 1.450 1.425 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.525 1.549 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 13440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 17451 1.46 - 2.93: 737 2.93 - 4.39: 91 4.39 - 5.85: 15 5.85 - 7.31: 3 Bond angle restraints: 18297 Sorted by residual: angle pdb=" O3' DT X 48 " pdb=" C3' DT X 48 " pdb=" C2' DT X 48 " ideal model delta sigma weight residual 111.50 117.10 -5.60 1.50e+00 4.44e-01 1.39e+01 angle pdb=" CA ARG A 768 " pdb=" CB ARG A 768 " pdb=" CG ARG A 768 " ideal model delta sigma weight residual 114.10 107.80 6.30 2.00e+00 2.50e-01 9.93e+00 angle pdb=" C3' DT X 48 " pdb=" O3' DT X 48 " pdb=" P DT X 49 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.89e+00 angle pdb=" C ASP A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta sigma weight residual 121.05 115.67 5.38 1.85e+00 2.92e-01 8.45e+00 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 109.70 105.34 4.36 1.50e+00 4.44e-01 8.45e+00 ... (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 - 0.046: 1564 0.046 - 0.093: 468 0.093 - 0.139: 109 0.139 - 0.186: 10 0.186 - 0.232: 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 -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.35e+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=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-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: 2.350 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.810 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13445 Z= 0.156 Angle : 0.681 7.314 18297 Z= 0.406 Chirality : 0.046 0.232 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 aren 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 covalent geometry : bond 0.00349 (13445) covalent geometry : angle 0.68121 (18297) hydrogen bonds : bond 0.19775 ( 619) hydrogen bonds : angle 8.05052 ( 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 : 0.503 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: 0.1623 time to fit residues: 68.0167 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 : 0.562 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 366 HIS A 416 HIS A 710 HIS ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** 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 = 0.4158 r_free = 0.4158 target = 0.183363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139250 restraints weight = 16522.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137230 restraints weight = 21531.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138708 restraints weight = 21333.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138850 restraints weight = 16385.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138988 restraints weight = 15946.830| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13445 Z= 0.164 Angle : 0.653 8.341 18297 Z= 0.346 Chirality : 0.042 0.175 2152 Planarity : 0.004 0.043 2165 Dihedral : 14.879 162.247 2180 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.55 % Allowed : 6.71 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.20), residues: 1550 helix: -0.71 (0.16), residues: 856 sheet: 0.50 (0.41), residues: 142 loop : 0.55 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 522 TYR 0.013 0.002 TYR A 171 PHE 0.016 0.002 PHE B 642 TRP 0.023 0.002 TRP A 661 HIS 0.006 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00379 (13445) covalent geometry : angle 0.65320 (18297) hydrogen bonds : bond 0.04496 ( 619) hydrogen bonds : angle 4.93547 ( 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 235 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.474 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: 0.8189 (mp) cc_final: 0.7722 (tp) REVERT: B 395 ARG cc_start: 0.7550 (mtt-85) cc_final: 0.7266 (mtt-85) REVERT: B 530 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (t) outliers start: 21 outliers final: 12 residues processed: 224 average time/residue: 0.1476 time to fit residues: 45.7983 Evaluate side-chains 180 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU 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 85 HIS Chi-restraints excluded: chain B residue 292 LEU 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 758 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4135 r_free = 0.4135 target = 0.181639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137492 restraints weight = 16328.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136093 restraints weight = 17440.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136795 restraints weight = 18027.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137480 restraints weight = 14730.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137832 restraints weight = 13443.564| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13445 Z= 0.131 Angle : 0.594 8.919 18297 Z= 0.311 Chirality : 0.040 0.226 2152 Planarity : 0.004 0.047 2165 Dihedral : 14.737 162.848 2180 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.62 % Allowed : 9.66 % 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 aren not related in a simple way. whole: 0.15 (0.21), residues: 1550 helix: -0.02 (0.17), residues: 858 sheet: 0.70 (0.41), residues: 142 loop : 0.48 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 843 TYR 0.013 0.001 TYR A 171 PHE 0.014 0.001 PHE B 415 TRP 0.016 0.001 TRP A 661 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00299 (13445) covalent geometry : angle 0.59381 (18297) hydrogen bonds : bond 0.03751 ( 619) hydrogen bonds : angle 4.61101 ( 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 210 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.514 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: 0.8223 (mp) cc_final: 0.7764 (tp) REVERT: A 331 TYR cc_start: 0.7815 (t80) cc_final: 0.6895 (t80) REVERT: A 391 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6151 (mtm) REVERT: A 655 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 391 MET cc_start: 0.7474 (tpp) cc_final: 0.7143 (tpp) REVERT: B 530 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (t) REVERT: B 784 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7967 (ttm-80) outliers start: 22 outliers final: 10 residues processed: 199 average time/residue: 0.1477 time to fit residues: 40.9130 Evaluate side-chains 177 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 391 MET 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 240 ILE 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 758 TYR Chi-restraints excluded: chain B residue 823 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4177 r_free = 0.4177 target = 0.185026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145232 restraints weight = 16582.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143428 restraints weight = 25934.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144545 restraints weight = 25086.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143841 restraints weight = 18721.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144252 restraints weight = 18563.702| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13445 Z= 0.144 Angle : 0.586 8.417 18297 Z= 0.305 Chirality : 0.040 0.245 2152 Planarity : 0.004 0.042 2165 Dihedral : 14.726 162.535 2180 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.99 % Allowed : 11.36 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1550 helix: 0.23 (0.18), residues: 854 sheet: 0.72 (0.42), residues: 142 loop : 0.32 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 522 TYR 0.013 0.001 TYR A 171 PHE 0.019 0.002 PHE B 181 TRP 0.011 0.001 TRP A 661 HIS 0.006 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00335 (13445) covalent geometry : angle 0.58555 (18297) hydrogen bonds : bond 0.03621 ( 619) hydrogen bonds : angle 4.43044 ( 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 200 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 293 LEU cc_start: 0.8115 (mp) cc_final: 0.7824 (tp) REVERT: A 469 LEU cc_start: 0.8187 (tp) cc_final: 0.7917 (tp) REVERT: A 655 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8537 (m) outliers start: 27 outliers final: 14 residues processed: 190 average time/residue: 0.1319 time to fit residues: 35.6473 Evaluate side-chains 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 484 LYS 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 240 ILE 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 530 SER Chi-restraints excluded: chain B residue 587 MET 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: 0.7980 chunk 71 optimal weight: 9.9990 chunk 38 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 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 = 0.4185 r_free = 0.4185 target = 0.185736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145474 restraints weight = 16669.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143494 restraints weight = 27889.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145060 restraints weight = 24784.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144966 restraints weight = 17794.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145170 restraints weight = 17520.873| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13445 Z= 0.124 Angle : 0.573 9.519 18297 Z= 0.296 Chirality : 0.040 0.236 2152 Planarity : 0.004 0.040 2165 Dihedral : 14.577 162.917 2178 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.84 % Allowed : 12.61 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.21), residues: 1550 helix: 0.46 (0.18), residues: 854 sheet: 0.70 (0.42), residues: 146 loop : 0.40 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 395 TYR 0.011 0.001 TYR A 171 PHE 0.014 0.001 PHE B 181 TRP 0.011 0.001 TRP A 661 HIS 0.007 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00284 (13445) covalent geometry : angle 0.57288 (18297) hydrogen bonds : bond 0.03431 ( 619) hydrogen bonds : angle 4.26970 ( 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 200 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8108 (mp) cc_final: 0.7850 (tp) REVERT: A 655 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 753 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6794 (mm-40) outliers start: 25 outliers final: 14 residues processed: 189 average time/residue: 0.1234 time to fit residues: 33.4526 Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 356 ILE 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 292 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 587 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 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 = 0.4174 r_free = 0.4174 target = 0.184551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145210 restraints weight = 16656.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143980 restraints weight = 24839.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144460 restraints weight = 23401.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143850 restraints weight = 18453.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144181 restraints weight = 18593.915| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4071 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= 0.156 Angle : 0.585 10.046 18297 Z= 0.303 Chirality : 0.041 0.241 2152 Planarity : 0.004 0.047 2165 Dihedral : 14.593 163.586 2178 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.14 % Allowed : 13.35 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1550 helix: 0.44 (0.18), residues: 852 sheet: 0.64 (0.42), residues: 146 loop : 0.30 (0.27), residues: 552 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 0.016 0.002 PHE A 765 TRP 0.008 0.001 TRP A 661 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00370 (13445) covalent geometry : angle 0.58451 (18297) hydrogen bonds : bond 0.03578 ( 619) hydrogen bonds : angle 4.29466 ( 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: 29 poor density : 167 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 293 LEU cc_start: 0.8080 (mp) cc_final: 0.7788 (tp) REVERT: A 655 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (m) REVERT: B 101 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7881 (mm) outliers start: 29 outliers final: 15 residues processed: 185 average time/residue: 0.1278 time to fit residues: 34.0314 Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 290 VAL Chi-restraints excluded: chain A residue 356 ILE 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 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 530 SER Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 ASN 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 = 0.4147 r_free = 0.4147 target = 0.181940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143936 restraints weight = 16779.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142071 restraints weight = 27730.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141855 restraints weight = 28942.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141175 restraints weight = 21066.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141787 restraints weight = 19037.562| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13445 Z= 0.225 Angle : 0.663 10.145 18297 Z= 0.341 Chirality : 0.044 0.249 2152 Planarity : 0.005 0.058 2165 Dihedral : 14.709 164.246 2178 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.43 % Allowed : 14.45 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1550 helix: 0.14 (0.17), residues: 850 sheet: 0.36 (0.42), residues: 150 loop : 0.04 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 705 TYR 0.015 0.002 TYR B 113 PHE 0.026 0.002 PHE A 765 TRP 0.041 0.002 TRP A 95 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00542 (13445) covalent geometry : angle 0.66284 (18297) hydrogen bonds : bond 0.04143 ( 619) hydrogen bonds : angle 4.54412 ( 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 197 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 293 LEU cc_start: 0.8131 (mp) cc_final: 0.7861 (tt) REVERT: A 469 LEU cc_start: 0.8236 (tp) cc_final: 0.8019 (tp) REVERT: A 640 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6838 (pttt) REVERT: A 803 ASN cc_start: 0.7484 (m110) cc_final: 0.6956 (p0) REVERT: B 101 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 392 ASP cc_start: 0.6195 (t70) cc_final: 0.5972 (t0) REVERT: B 396 ARG cc_start: 0.7455 (ptt180) cc_final: 0.7139 (ptt-90) REVERT: B 436 LEU cc_start: 0.7834 (mt) cc_final: 0.7581 (mp) REVERT: B 672 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8088 (tp) outliers start: 33 outliers final: 16 residues processed: 184 average time/residue: 0.1239 time to fit residues: 32.6152 Evaluate side-chains 180 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 356 ILE 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 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 530 SER Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 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 = 0.185314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146014 restraints weight = 16559.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145500 restraints weight = 24211.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146133 restraints weight = 21673.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145394 restraints weight = 17873.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145631 restraints weight = 17358.949| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4398 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= 0.128 Angle : 0.574 8.758 18297 Z= 0.298 Chirality : 0.040 0.190 2152 Planarity : 0.004 0.046 2165 Dihedral : 14.552 164.545 2178 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.70 % Allowed : 15.49 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.22), residues: 1550 helix: 0.56 (0.18), residues: 852 sheet: 0.42 (0.42), residues: 150 loop : 0.01 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.010 0.001 TYR A 171 PHE 0.014 0.001 PHE B 287 TRP 0.039 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00296 (13445) covalent geometry : angle 0.57371 (18297) hydrogen bonds : bond 0.03257 ( 619) hydrogen bonds : angle 4.20399 ( 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 190 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8124 (tt) REVERT: A 293 LEU cc_start: 0.8001 (mp) cc_final: 0.7791 (tp) REVERT: A 655 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8531 (m) REVERT: A 803 ASN cc_start: 0.7470 (m110) cc_final: 0.6961 (p0) REVERT: B 101 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 436 LEU cc_start: 0.7763 (mt) cc_final: 0.7540 (mp) REVERT: B 784 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8128 (ttm-80) outliers start: 23 outliers final: 15 residues processed: 178 average time/residue: 0.1374 time to fit residues: 34.3761 Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL 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 655 THR Chi-restraints excluded: chain A residue 815 PHE 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 530 SER Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4186 r_free = 0.4186 target = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148781 restraints weight = 16570.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148108 restraints weight = 20803.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147487 restraints weight = 22880.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146443 restraints weight = 19211.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147110 restraints weight = 18842.726| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13445 Z= 0.122 Angle : 0.575 10.407 18297 Z= 0.296 Chirality : 0.039 0.189 2152 Planarity : 0.004 0.045 2165 Dihedral : 14.486 164.825 2178 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.70 % Allowed : 15.78 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.22), residues: 1550 helix: 0.72 (0.18), residues: 852 sheet: 0.48 (0.42), residues: 150 loop : 0.01 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 856 TYR 0.010 0.001 TYR A 331 PHE 0.012 0.001 PHE B 181 TRP 0.043 0.001 TRP A 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00283 (13445) covalent geometry : angle 0.57539 (18297) hydrogen bonds : bond 0.03141 ( 619) hydrogen bonds : angle 4.16526 ( 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 191 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.576 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: 0.8588 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 640 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6476 (pttt) REVERT: A 655 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (m) REVERT: A 803 ASN cc_start: 0.7410 (m110) cc_final: 0.6957 (p0) REVERT: B 101 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7863 (mm) REVERT: B 436 LEU cc_start: 0.7763 (mt) cc_final: 0.7540 (mp) REVERT: B 784 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8138 (ttm-80) outliers start: 23 outliers final: 12 residues processed: 181 average time/residue: 0.1427 time to fit residues: 36.2653 Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL 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 655 THR Chi-restraints excluded: chain A residue 815 PHE 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 527 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4187 r_free = 0.4187 target = 0.185886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146303 restraints weight = 16487.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145072 restraints weight = 25783.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145460 restraints weight = 25444.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144303 restraints weight = 20376.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145021 restraints weight = 18240.502| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13445 Z= 0.128 Angle : 0.591 10.688 18297 Z= 0.303 Chirality : 0.040 0.186 2152 Planarity : 0.004 0.045 2165 Dihedral : 14.478 164.810 2178 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 16.37 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.22), residues: 1550 helix: 0.79 (0.18), residues: 852 sheet: 0.54 (0.43), residues: 150 loop : 0.02 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.015 0.001 TYR A 239 PHE 0.019 0.001 PHE B 287 TRP 0.046 0.001 TRP A 95 HIS 0.008 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00296 (13445) covalent geometry : angle 0.59066 (18297) hydrogen bonds : bond 0.03212 ( 619) hydrogen bonds : angle 4.15097 ( 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 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 640 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6155 (pttt) REVERT: A 655 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8465 (m) REVERT: A 803 ASN cc_start: 0.7496 (m110) cc_final: 0.6983 (p0) REVERT: B 101 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7883 (mm) REVERT: B 784 ARG cc_start: 0.8472 (ttm110) cc_final: 0.8156 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 167 average time/residue: 0.1316 time to fit residues: 31.5360 Evaluate side-chains 171 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE 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 655 THR Chi-restraints excluded: chain A residue 815 PHE 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 527 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4181 r_free = 0.4181 target = 0.185323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146292 restraints weight = 16462.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145301 restraints weight = 23079.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145955 restraints weight = 22738.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145735 restraints weight = 19957.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145798 restraints weight = 20351.131| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4701 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= 0.133 Angle : 0.590 10.433 18297 Z= 0.301 Chirality : 0.040 0.190 2152 Planarity : 0.004 0.046 2165 Dihedral : 14.471 164.977 2178 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.33 % Allowed : 16.37 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.22), residues: 1550 helix: 0.80 (0.18), residues: 852 sheet: 0.54 (0.44), residues: 150 loop : -0.00 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 396 TYR 0.015 0.001 TYR A 239 PHE 0.018 0.001 PHE B 287 TRP 0.044 0.001 TRP A 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00311 (13445) covalent geometry : angle 0.58975 (18297) hydrogen bonds : bond 0.03206 ( 619) hydrogen bonds : angle 4.14047 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2041.70 seconds wall clock time: 36 minutes 14.77 seconds (2174.77 seconds total)