Starting phenix.real_space_refine on Thu Aug 6 02:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2026/9bh8_44536.map" } resolution = 3.6 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= 0.034 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 43 5.49 5 S 78 5.16 5 C 8229 2.51 5 N 2210 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13051 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: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 215 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3} Unresolved non-hydrogen planarities: 58 Chain: "Y" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 430 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1, ' DT:plan': 12, ' DG:plan': 5, ' DG:plan2': 5, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2} Unresolved non-hydrogen planarities: 227 Time building chain proxies: 2.25, per 1000 atoms: 0.17 Number of scatterers: 13051 At special positions: 0 Unit cell: (125.783, 149.94, 89.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 43 15.00 O 2491 8.00 N 2210 7.00 C 8229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 406.6 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 60.5% alpha, 9.0% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.599A 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 101 Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.312A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.701A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 246 removed outlier: 3.675A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.755A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 368 removed outlier: 3.541A pdb=" N ASP A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.650A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.834A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.885A pdb=" N ILE A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 578 through 592 removed outlier: 4.228A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.102A 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 639 removed outlier: 4.316A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 removed outlier: 3.685A pdb=" N LEU A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 690 through 700 removed outlier: 4.730A pdb=" N ARG A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.575A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.077A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 768 removed outlier: 4.049A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 Processing helix chain 'A' and resid 793 through 801 removed outlier: 3.541A pdb=" N LEU A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 removed outlier: 3.957A 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 837 removed outlier: 4.617A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 4.403A pdb=" N GLU A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 860 " --> pdb=" O ARG A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 892 removed outlier: 3.889A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.026A pdb=" N GLY B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.089A pdb=" N LEU B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) 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: 3.948A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.262A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 Processing helix chain 'B' and resid 383 through 396 removed outlier: 3.769A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.604A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) 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 478 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.534A pdb=" N GLY B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.067A 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 558 through 563 Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.967A pdb=" N GLU B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 621 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.667A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 677 through 688 removed outlier: 4.573A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.843A pdb=" N ARG B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 730 removed outlier: 3.653A pdb=" N HIS B 716 " --> pdb=" O GLN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.595A pdb=" N ASN B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 739 " --> pdb=" O ARG B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.704A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 780 removed outlier: 4.159A pdb=" N LEU B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 784 Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 803 through 815 removed outlier: 4.042A pdb=" N VAL B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 825 through 835 Processing helix chain 'B' and resid 850 through 858 removed outlier: 3.989A pdb=" N ARG B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 892 removed outlier: 3.825A pdb=" N ALA B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 892 " --> pdb=" O GLN B 888 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.744A pdb=" N ASP A 169 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR A 190 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR A 171 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN A 110 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR A 283 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 112 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.552A pdb=" N SER A 295 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N CYS A 496 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS A 297 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP A 304 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 309 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.574A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 414 " --> pdb=" O ALA A 441 " (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: 6.366A pdb=" N ASP B 169 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR B 190 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B 171 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 139 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 212 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY B 211 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL B 262 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 213 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N MET B 264 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 215 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 293 removed outlier: 6.583A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 495 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 459 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 340 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA B 442 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 342 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AB1, first strand: chain 'B' and resid 595 through 598 643 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3921 1.34 - 1.45: 1768 1.45 - 1.57: 7432 1.57 - 1.69: 85 1.69 - 1.81: 124 Bond restraints: 13330 Sorted by residual: bond pdb=" C3' DT X 48 " pdb=" C2' DT X 48 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.62e+01 bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.80e+01 bond pdb=" C3' DT Y 39 " pdb=" C2' DT Y 39 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.59e+01 bond pdb=" C1' DT X 45 " pdb=" N1 DT X 45 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" O4' DG Y 41 " pdb=" C1' DG Y 41 " ideal model delta sigma weight residual 1.420 1.379 0.041 1.10e-02 8.26e+03 1.37e+01 ... (remaining 13325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17207 1.39 - 2.78: 768 2.78 - 4.17: 113 4.17 - 5.56: 27 5.56 - 6.95: 5 Bond angle restraints: 18120 Sorted by residual: angle pdb=" O5' DG X 54 " pdb=" C5' DG X 54 " pdb=" C4' DG X 54 " ideal model delta sigma weight residual 109.40 113.60 -4.20 8.00e-01 1.56e+00 2.76e+01 angle pdb=" O4' DA Y 29 " pdb=" C1' DA Y 29 " pdb=" C2' DA Y 29 " ideal model delta sigma weight residual 105.90 101.93 3.97 8.00e-01 1.56e+00 2.46e+01 angle pdb=" O4' DT Y 39 " pdb=" C1' DT Y 39 " pdb=" N1 DT Y 39 " ideal model delta sigma weight residual 108.00 104.55 3.45 7.00e-01 2.04e+00 2.44e+01 angle pdb=" O4' DT Y 47 " pdb=" C4' DT Y 47 " pdb=" C3' DT Y 47 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 110.10 105.55 4.55 1.00e+00 1.00e+00 2.07e+01 ... (remaining 18115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.24: 7750 30.24 - 60.49: 312 60.49 - 90.73: 27 90.73 - 120.98: 0 120.98 - 151.22: 1 Dihedral angle restraints: 8090 sinusoidal: 3530 harmonic: 4560 Sorted by residual: dihedral pdb=" CA THR B 662 " pdb=" C THR B 662 " pdb=" N THR B 663 " pdb=" CA THR B 663 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ARG B 705 " pdb=" C ARG B 705 " pdb=" N THR B 706 " pdb=" CA THR B 706 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+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 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 8087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1682 0.051 - 0.102: 355 0.102 - 0.154: 85 0.154 - 0.205: 5 0.205 - 0.256: 3 Chirality restraints: 2130 Sorted by residual: chirality pdb=" C4' DG X 50 " pdb=" C5' DG X 50 " pdb=" O4' DG X 50 " pdb=" C3' DG X 50 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' DC Y 19 " pdb=" C4' DC Y 19 " pdb=" O3' DC Y 19 " pdb=" C2' DC Y 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4' DG Y 41 " pdb=" C5' DG Y 41 " pdb=" O4' DG Y 41 " pdb=" C3' DG Y 41 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2127 not shown) Planarity restraints: 2161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 37 " 0.017 2.00e-02 2.50e+03 2.30e-02 1.45e+01 pdb=" N9 DA Y 37 " -0.062 2.00e-02 2.50e+03 pdb=" C8 DA Y 37 " 0.039 2.00e-02 2.50e+03 pdb=" N7 DA Y 37 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA Y 37 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA Y 37 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA Y 37 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA Y 37 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA Y 37 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA Y 37 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA Y 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 38 " 0.000 2.00e-02 2.50e+03 1.90e-02 1.08e+01 pdb=" N9 DG Y 38 " -0.046 2.00e-02 2.50e+03 pdb=" C8 DG Y 38 " 0.045 2.00e-02 2.50e+03 pdb=" N7 DG Y 38 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG Y 38 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG Y 38 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG Y 38 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG Y 38 " 0.000 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 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG Y 38 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 39 " -0.037 2.00e-02 2.50e+03 1.85e-02 8.56e+00 pdb=" N1 DT Y 39 " 0.043 2.00e-02 2.50e+03 pdb=" C2 DT Y 39 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT Y 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT Y 39 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT Y 39 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT Y 39 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT Y 39 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT Y 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT Y 39 " 0.004 2.00e-02 2.50e+03 ... (remaining 2158 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3530 2.83 - 3.35: 12700 3.35 - 3.86: 20172 3.86 - 4.38: 24860 4.38 - 4.90: 41104 Nonbonded interactions: 102366 Sorted by model distance: nonbonded pdb=" O LEU B 329 " pdb=" NH1 ARG B 456 " model vdw 2.310 3.120 nonbonded pdb=" O LEU A 329 " pdb=" NH1 ARG A 456 " model vdw 2.339 3.120 nonbonded pdb=" OD2 ASP A 634 " pdb=" NH1 ARG A 718 " model vdw 2.345 3.120 nonbonded pdb=" NZ LYS A 640 " pdb=" OE2 GLU B 848 " model vdw 2.356 3.120 nonbonded pdb=" NH1 ARG A 455 " pdb=" OD2 ASP A 487 " model vdw 2.356 3.120 ... (remaining 102361 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: 2.200 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 0.053 13330 Z= 0.242 Angle : 0.673 6.951 18120 Z= 0.451 Chirality : 0.046 0.256 2130 Planarity : 0.008 0.085 2161 Dihedral : 15.494 151.221 5130 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.15 % Allowed : 0.22 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 1550 helix: -2.25 (0.13), residues: 868 sheet: 0.36 (0.38), residues: 154 loop : -0.31 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG B 711 TYR 0.030 0.005 TYR B 553 PHE 0.022 0.001 PHE B 815 TRP 0.018 0.002 TRP A 411 HIS 0.008 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.24 (13330) covalent geometry : angle 0.67275 / 0.45 (18120) hydrogen bonds : bond 0.20833 / 13.45 ( 639) hydrogen bonds : angle 7.98511 / 5.65 ( 1839) *********************** 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 324 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 0.447 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 THR cc_start: 0.7281 (p) cc_final: 0.6979 (p) REVERT: A 189 CYS cc_start: 0.7881 (t) cc_final: 0.7591 (m) REVERT: A 331 TYR cc_start: 0.8274 (t80) cc_final: 0.7851 (t80) REVERT: A 346 SER cc_start: 0.8431 (t) cc_final: 0.7628 (p) REVERT: A 619 LEU cc_start: 0.8307 (mp) cc_final: 0.7633 (mp) REVERT: A 639 MET cc_start: 0.9124 (mmm) cc_final: 0.8739 (mmt) REVERT: A 780 GLN cc_start: 0.7682 (tt0) cc_final: 0.7281 (tt0) REVERT: B 267 THR cc_start: 0.8514 (m) cc_final: 0.8311 (p) REVERT: B 563 MET cc_start: 0.7109 (mtp) cc_final: 0.6857 (mtm) REVERT: B 634 ASP cc_start: 0.7745 (m-30) cc_final: 0.7511 (m-30) REVERT: B 783 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7141 (pttt) REVERT: B 843 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6725 (ttp-110) outliers start: 2 outliers final: 1 residues processed: 324 average time/residue: 0.1251 time to fit residues: 54.9450 Evaluate side-chains 198 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 0.6980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 279 ASN A 337 ASN A 592 ASN A 816 HIS B 73 ASN B 195 ASN B 279 ASN B 406 GLN B 738 ASN B 816 HIS B 825 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141170 restraints weight = 18284.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140595 restraints weight = 21131.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140231 restraints weight = 17939.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139661 restraints weight = 16062.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140051 restraints weight = 14698.383| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13330 Z= 0.187 Angle : 0.721 9.922 18120 Z= 0.381 Chirality : 0.045 0.279 2130 Planarity : 0.005 0.068 2161 Dihedral : 15.115 152.230 2122 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.99 % Allowed : 7.89 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1550 helix: -0.88 (0.16), residues: 908 sheet: 0.25 (0.38), residues: 150 loop : 0.04 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 823 TYR 0.016 0.002 TYR B 303 PHE 0.029 0.002 PHE A 87 TRP 0.015 0.002 TRP A 661 HIS 0.011 0.002 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (13330) covalent geometry : angle 0.72095 / 0.38 (18120) hydrogen bonds : bond 0.05962 / 3.83 ( 639) hydrogen bonds : angle 5.29293 / 3.72 ( 1839) *********************** 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 240 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.318 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.7684 (t80) cc_final: 0.7358 (t80) REVERT: A 338 HIS cc_start: 0.6474 (m-70) cc_final: 0.5912 (m170) REVERT: A 346 SER cc_start: 0.8532 (t) cc_final: 0.7948 (p) REVERT: A 491 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: B 126 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7371 (mp0) REVERT: B 267 THR cc_start: 0.8432 (m) cc_final: 0.8203 (p) REVERT: B 563 MET cc_start: 0.6891 (mtp) cc_final: 0.6645 (mtm) REVERT: B 587 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6515 (tpp) REVERT: B 634 ASP cc_start: 0.7650 (m-30) cc_final: 0.7309 (m-30) REVERT: B 738 ASN cc_start: 0.8086 (m-40) cc_final: 0.7711 (m-40) REVERT: B 843 ARG cc_start: 0.7249 (mtp85) cc_final: 0.6645 (ttp-110) outliers start: 27 outliers final: 14 residues processed: 229 average time/residue: 0.1081 time to fit residues: 35.4663 Evaluate side-chains 188 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 729 ILE 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 41 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN A 338 HIS A 366 HIS A 710 HIS A 752 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 325 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141317 restraints weight = 18250.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140539 restraints weight = 21124.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140224 restraints weight = 18289.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138713 restraints weight = 19378.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139472 restraints weight = 16867.772| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13330 Z= 0.160 Angle : 0.670 13.304 18120 Z= 0.351 Chirality : 0.043 0.269 2130 Planarity : 0.005 0.093 2161 Dihedral : 14.918 150.370 2122 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.51 % Allowed : 10.32 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1550 helix: -0.44 (0.16), residues: 906 sheet: 0.04 (0.36), residues: 160 loop : 0.17 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 884 TYR 0.018 0.002 TYR B 303 PHE 0.045 0.002 PHE B 87 TRP 0.013 0.001 TRP A 666 HIS 0.006 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (13330) covalent geometry : angle 0.67021 / 0.35 (18120) hydrogen bonds : bond 0.04882 / 3.11 ( 639) hydrogen bonds : angle 4.79743 / 3.38 ( 1839) *********************** 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 212 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.391 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 331 TYR cc_start: 0.7668 (t80) cc_final: 0.7363 (t80) REVERT: A 346 SER cc_start: 0.8388 (t) cc_final: 0.7840 (p) REVERT: B 267 THR cc_start: 0.8434 (m) cc_final: 0.8154 (p) REVERT: B 563 MET cc_start: 0.6900 (mtp) cc_final: 0.6643 (mtm) REVERT: B 587 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6583 (tpp) REVERT: B 634 ASP cc_start: 0.7575 (m-30) cc_final: 0.7366 (m-30) REVERT: B 731 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 738 ASN cc_start: 0.7982 (m-40) cc_final: 0.7624 (m-40) REVERT: B 843 ARG cc_start: 0.7161 (mtp85) cc_final: 0.6584 (ttp-110) outliers start: 34 outliers final: 19 residues processed: 201 average time/residue: 0.1036 time to fit residues: 30.1097 Evaluate side-chains 182 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 451 ASN B 85 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.176411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138593 restraints weight = 18331.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136834 restraints weight = 25620.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137864 restraints weight = 24310.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137073 restraints weight = 19637.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137798 restraints weight = 19285.049| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13330 Z= 0.225 Angle : 0.691 12.500 18120 Z= 0.362 Chirality : 0.045 0.295 2130 Planarity : 0.004 0.043 2161 Dihedral : 14.978 149.278 2122 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.43 % Allowed : 11.21 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1550 helix: -0.39 (0.16), residues: 910 sheet: -0.28 (0.37), residues: 160 loop : 0.03 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 395 TYR 0.016 0.002 TYR B 303 PHE 0.018 0.002 PHE A 658 TRP 0.015 0.002 TRP A 588 HIS 0.011 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (13330) covalent geometry : angle 0.69070 / 0.36 (18120) hydrogen bonds : bond 0.04831 / 3.04 ( 639) hydrogen bonds : angle 4.75800 / 3.37 ( 1839) *********************** 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 213 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.570 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: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.7477 (t80) cc_final: 0.7217 (t80) REVERT: A 346 SER cc_start: 0.8432 (t) cc_final: 0.7887 (p) REVERT: A 718 ARG cc_start: 0.7618 (ttt180) cc_final: 0.6440 (ttt90) REVERT: A 776 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 185 ASP cc_start: 0.7878 (m-30) cc_final: 0.7555 (m-30) REVERT: B 401 LEU cc_start: 0.6834 (tp) cc_final: 0.6604 (tp) REVERT: B 563 MET cc_start: 0.7035 (mtp) cc_final: 0.6759 (mtm) REVERT: B 587 MET cc_start: 0.6887 (tpp) cc_final: 0.6587 (tpp) REVERT: B 634 ASP cc_start: 0.7990 (m-30) cc_final: 0.7667 (m-30) REVERT: B 731 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 738 ASN cc_start: 0.7961 (m-40) cc_final: 0.7627 (m-40) REVERT: B 843 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6759 (ttp-110) outliers start: 33 outliers final: 19 residues processed: 198 average time/residue: 0.1006 time to fit residues: 28.9100 Evaluate side-chains 183 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.178698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141491 restraints weight = 18619.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140076 restraints weight = 25110.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141663 restraints weight = 23214.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140412 restraints weight = 18957.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140917 restraints weight = 19801.775| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13330 Z= 0.158 Angle : 0.639 12.857 18120 Z= 0.333 Chirality : 0.043 0.263 2130 Planarity : 0.004 0.037 2161 Dihedral : 14.949 148.075 2122 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.88 % Allowed : 12.46 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1550 helix: -0.12 (0.17), residues: 912 sheet: -0.54 (0.39), residues: 142 loop : 0.01 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 395 TYR 0.012 0.001 TYR B 303 PHE 0.012 0.001 PHE A 432 TRP 0.011 0.001 TRP A 666 HIS 0.007 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (13330) covalent geometry : angle 0.63913 / 0.33 (18120) hydrogen bonds : bond 0.04298 / 2.72 ( 639) hydrogen bonds : angle 4.53453 / 3.21 ( 1839) *********************** 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 215 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.340 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 331 TYR cc_start: 0.7576 (t80) cc_final: 0.7352 (t80) REVERT: A 346 SER cc_start: 0.8345 (t) cc_final: 0.7782 (p) REVERT: A 718 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6215 (tpt-90) REVERT: A 776 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 185 ASP cc_start: 0.7783 (m-30) cc_final: 0.7449 (m-30) REVERT: B 587 MET cc_start: 0.6886 (tpp) cc_final: 0.6532 (tpp) REVERT: B 634 ASP cc_start: 0.8213 (m-30) cc_final: 0.7912 (m-30) REVERT: B 731 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 738 ASN cc_start: 0.7893 (m-40) cc_final: 0.7558 (m-40) REVERT: B 843 ARG cc_start: 0.7198 (mtp85) cc_final: 0.6761 (ttp-110) outliers start: 39 outliers final: 23 residues processed: 200 average time/residue: 0.1179 time to fit residues: 33.5058 Evaluate side-chains 183 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.177527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136958 restraints weight = 18455.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135073 restraints weight = 26571.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136225 restraints weight = 23861.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136972 restraints weight = 18930.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137014 restraints weight = 18200.786| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13330 Z= 0.188 Angle : 0.668 12.651 18120 Z= 0.345 Chirality : 0.043 0.243 2130 Planarity : 0.004 0.039 2161 Dihedral : 14.971 147.168 2122 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.43 % Allowed : 12.98 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1550 helix: -0.09 (0.17), residues: 914 sheet: -0.69 (0.39), residues: 142 loop : -0.01 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 395 TYR 0.012 0.001 TYR B 303 PHE 0.013 0.002 PHE A 432 TRP 0.012 0.001 TRP A 588 HIS 0.013 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (13330) covalent geometry : angle 0.66826 / 0.34 (18120) hydrogen bonds : bond 0.04335 / 2.73 ( 639) hydrogen bonds : angle 4.52746 / 3.21 ( 1839) *********************** 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 201 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.383 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: symmetry clash REVERT: A 346 SER cc_start: 0.8287 (t) cc_final: 0.7746 (p) REVERT: A 718 ARG cc_start: 0.7689 (ttt180) cc_final: 0.6393 (tpt-90) REVERT: A 776 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 185 ASP cc_start: 0.7794 (m-30) cc_final: 0.7457 (m-30) REVERT: B 587 MET cc_start: 0.6962 (tpp) cc_final: 0.6644 (tpp) REVERT: B 634 ASP cc_start: 0.8231 (m-30) cc_final: 0.7867 (m-30) REVERT: B 738 ASN cc_start: 0.7898 (m-40) cc_final: 0.7565 (m-40) REVERT: B 806 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: B 843 ARG cc_start: 0.7166 (mtp85) cc_final: 0.6768 (ttp-110) outliers start: 33 outliers final: 22 residues processed: 189 average time/residue: 0.1005 time to fit residues: 27.8321 Evaluate side-chains 186 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 806 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138484 restraints weight = 18308.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136408 restraints weight = 26198.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139144 restraints weight = 21798.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138724 restraints weight = 16489.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138941 restraints weight = 16613.975| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13330 Z= 0.143 Angle : 0.643 12.338 18120 Z= 0.329 Chirality : 0.042 0.300 2130 Planarity : 0.004 0.041 2161 Dihedral : 14.922 146.113 2122 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.84 % Allowed : 14.60 % Favored : 83.55 % 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 are not related in a simple way. whole: -0.11 (0.21), residues: 1550 helix: 0.10 (0.17), residues: 916 sheet: -0.24 (0.39), residues: 150 loop : 0.01 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 395 TYR 0.035 0.001 TYR A 331 PHE 0.025 0.001 PHE A 93 TRP 0.010 0.001 TRP A 588 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13330) covalent geometry : angle 0.64259 / 0.33 (18120) hydrogen bonds : bond 0.04073 / 2.58 ( 639) hydrogen bonds : angle 4.39815 / 3.12 ( 1839) *********************** 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 199 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.329 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 331 TYR cc_start: 0.7866 (t80) cc_final: 0.7521 (t80) REVERT: A 346 SER cc_start: 0.8272 (t) cc_final: 0.7798 (p) REVERT: A 718 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6234 (tpt-90) REVERT: A 776 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 157 LEU cc_start: 0.8131 (mt) cc_final: 0.7874 (mt) REVERT: B 587 MET cc_start: 0.6939 (tpp) cc_final: 0.6617 (tpp) REVERT: B 634 ASP cc_start: 0.8051 (m-30) cc_final: 0.7725 (m-30) REVERT: B 738 ASN cc_start: 0.7853 (m-40) cc_final: 0.7519 (m-40) REVERT: B 806 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6684 (mtp85) REVERT: B 843 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6750 (ttp-110) outliers start: 25 outliers final: 18 residues processed: 187 average time/residue: 0.1023 time to fit residues: 27.8204 Evaluate side-chains 182 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 806 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 835 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.178015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135569 restraints weight = 18261.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134039 restraints weight = 17340.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135546 restraints weight = 15042.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136457 restraints weight = 12812.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136428 restraints weight = 11875.771| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13330 Z= 0.133 Angle : 0.648 15.546 18120 Z= 0.331 Chirality : 0.042 0.345 2130 Planarity : 0.004 0.085 2161 Dihedral : 14.830 144.938 2122 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 15.49 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1550 helix: 0.19 (0.17), residues: 914 sheet: -0.16 (0.38), residues: 150 loop : 0.01 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 884 TYR 0.020 0.001 TYR A 331 PHE 0.020 0.001 PHE A 93 TRP 0.017 0.001 TRP A 95 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13330) covalent geometry : angle 0.64830 / 0.33 (18120) hydrogen bonds : bond 0.03892 / 2.46 ( 639) hydrogen bonds : angle 4.34078 / 3.09 ( 1839) *********************** 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 202 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.408 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 212 MET cc_start: 0.7578 (ttm) cc_final: 0.7125 (ttt) REVERT: A 331 TYR cc_start: 0.8168 (t80) cc_final: 0.7940 (t80) REVERT: A 346 SER cc_start: 0.8039 (t) cc_final: 0.7594 (p) REVERT: A 718 ARG cc_start: 0.7559 (ttt180) cc_final: 0.6337 (tpt-90) REVERT: A 776 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 157 LEU cc_start: 0.8148 (mt) cc_final: 0.7875 (mt) REVERT: B 233 LEU cc_start: 0.7961 (tt) cc_final: 0.7751 (tt) REVERT: B 587 MET cc_start: 0.6999 (tpp) cc_final: 0.6624 (tpp) REVERT: B 634 ASP cc_start: 0.8025 (m-30) cc_final: 0.7701 (m-30) REVERT: B 738 ASN cc_start: 0.7866 (m-40) cc_final: 0.7579 (m-40) REVERT: B 806 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6621 (mtp85) REVERT: B 843 ARG cc_start: 0.7270 (mtp85) cc_final: 0.6757 (ttp-110) outliers start: 29 outliers final: 22 residues processed: 190 average time/residue: 0.1173 time to fit residues: 32.5752 Evaluate side-chains 185 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 121 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 835 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135089 restraints weight = 18400.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132782 restraints weight = 16980.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134209 restraints weight = 14613.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134848 restraints weight = 12830.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135070 restraints weight = 11693.560| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13330 Z= 0.126 Angle : 0.641 14.466 18120 Z= 0.327 Chirality : 0.044 0.639 2130 Planarity : 0.004 0.097 2161 Dihedral : 14.780 144.188 2122 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.84 % Allowed : 15.27 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1550 helix: 0.26 (0.17), residues: 912 sheet: -0.08 (0.38), residues: 150 loop : -0.00 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 395 TYR 0.015 0.001 TYR A 331 PHE 0.021 0.001 PHE A 432 TRP 0.028 0.001 TRP A 863 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13330) covalent geometry : angle 0.64058 / 0.33 (18120) hydrogen bonds : bond 0.03758 / 2.37 ( 639) hydrogen bonds : angle 4.30514 / 3.06 ( 1839) *********************** 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 195 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.476 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 212 MET cc_start: 0.7651 (ttm) cc_final: 0.7159 (ttt) REVERT: A 331 TYR cc_start: 0.8414 (t80) cc_final: 0.8151 (t80) REVERT: A 346 SER cc_start: 0.7836 (t) cc_final: 0.7395 (p) REVERT: A 718 ARG cc_start: 0.7529 (ttt180) cc_final: 0.6286 (tpt-90) REVERT: A 776 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8122 (tt) REVERT: B 157 LEU cc_start: 0.8136 (mt) cc_final: 0.7840 (mt) REVERT: B 587 MET cc_start: 0.6971 (tpp) cc_final: 0.6598 (tpp) REVERT: B 634 ASP cc_start: 0.8021 (m-30) cc_final: 0.7675 (m-30) REVERT: B 738 ASN cc_start: 0.7821 (m-40) cc_final: 0.7508 (m-40) REVERT: B 806 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6628 (mtp85) REVERT: B 843 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6736 (ttp-110) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.1213 time to fit residues: 32.3904 Evaluate side-chains 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 835 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135728 restraints weight = 18440.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133794 restraints weight = 16780.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135594 restraints weight = 14957.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136113 restraints weight = 12276.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136269 restraints weight = 11329.726| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13330 Z= 0.132 Angle : 0.653 14.226 18120 Z= 0.330 Chirality : 0.043 0.487 2130 Planarity : 0.004 0.084 2161 Dihedral : 14.733 143.261 2122 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 16.00 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1550 helix: 0.30 (0.17), residues: 912 sheet: 0.01 (0.38), residues: 150 loop : -0.06 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 395 TYR 0.013 0.001 TYR A 331 PHE 0.021 0.001 PHE A 432 TRP 0.019 0.001 TRP A 95 HIS 0.005 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13330) covalent geometry : angle 0.65269 / 0.33 (18120) hydrogen bonds : bond 0.03754 / 2.38 ( 639) hydrogen bonds : angle 4.27252 / 3.05 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.671 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.7671 (ttm) cc_final: 0.7223 (ttt) REVERT: A 331 TYR cc_start: 0.8217 (t80) cc_final: 0.7996 (t80) REVERT: A 346 SER cc_start: 0.7867 (t) cc_final: 0.7395 (p) REVERT: A 645 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 718 ARG cc_start: 0.7546 (ttt180) cc_final: 0.6317 (tpt-90) REVERT: A 776 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 587 MET cc_start: 0.6977 (tpp) cc_final: 0.6608 (tpp) REVERT: B 634 ASP cc_start: 0.8014 (m-30) cc_final: 0.7664 (m-30) REVERT: B 738 ASN cc_start: 0.7817 (m-40) cc_final: 0.7532 (m-40) REVERT: B 806 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6652 (mtp85) REVERT: B 843 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6739 (ttp-110) outliers start: 19 outliers final: 15 residues processed: 181 average time/residue: 0.1163 time to fit residues: 30.8520 Evaluate side-chains 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 835 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.178572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134884 restraints weight = 18204.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133620 restraints weight = 16490.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135208 restraints weight = 14510.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135715 restraints weight = 12405.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135872 restraints weight = 11424.424| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13330 Z= 0.132 Angle : 0.654 14.014 18120 Z= 0.330 Chirality : 0.042 0.378 2130 Planarity : 0.004 0.082 2161 Dihedral : 14.705 142.811 2122 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.70 % Allowed : 16.00 % 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 are not related in a simple way. whole: 0.16 (0.21), residues: 1550 helix: 0.35 (0.17), residues: 912 sheet: 0.12 (0.38), residues: 150 loop : -0.05 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 395 TYR 0.015 0.001 TYR B 239 PHE 0.020 0.001 PHE A 432 TRP 0.018 0.001 TRP A 95 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13330) covalent geometry : angle 0.65400 / 0.33 (18120) hydrogen bonds : bond 0.03694 / 2.34 ( 639) hydrogen bonds : angle 4.25507 / 3.04 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.91 seconds wall clock time: 34 minutes 13.41 seconds (2053.41 seconds total)