Starting phenix.real_space_refine on Fri Jul 3 08:06:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh8_44536/07_2026/9bh8_44536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh8_44536/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh8_44536/07_2026/9bh8_44536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh8_44536/07_2026/9bh8_44536.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh8_44536/07_2026/9bh8_44536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh8_44536/07_2026/9bh8_44536.cif" } 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-dev-6108/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: 3.07, per 1000 atoms: 0.24 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: 1.17 Conformation dependent library (CDL) restraints added in 635.8 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: 1.42 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: 2.36 Time building geometry restraints manager: 1.55 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: 17217 1.39 - 2.78: 758 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- 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 : 0.670 6.951 18120 Z= 0.448 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 0.67045 / 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 : 0.515 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: 0.7588 (m) REVERT: A 331 TYR cc_start: 0.8274 (t80) cc_final: 0.7850 (t80) REVERT: A 346 SER cc_start: 0.8431 (t) cc_final: 0.7678 (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: 0.7282 (tt0) REVERT: B 267 THR cc_start: 0.8514 (m) cc_final: 0.8310 (p) REVERT: B 563 MET cc_start: 0.7109 (mtp) cc_final: 0.6858 (mtm) REVERT: B 634 ASP cc_start: 0.7745 (m-30) cc_final: 0.7509 (m-30) REVERT: B 783 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7140 (pttt) REVERT: B 843 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6724 (ttp-110) outliers start: 2 outliers final: 1 residues processed: 324 average time/residue: 0.1534 time to fit residues: 66.9360 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 : 0.484 ------------------------------------------------------------------------------- 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 338 HIS A 592 ASN A 710 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135479 restraints weight = 18174.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135363 restraints weight = 20083.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136945 restraints weight = 16397.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136949 restraints weight = 13661.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136967 restraints weight = 13683.878| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13330 Z= 0.184 Angle : 0.720 10.215 18120 Z= 0.380 Chirality : 0.045 0.255 2130 Planarity : 0.005 0.066 2161 Dihedral : 15.106 152.968 2122 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.99 % Allowed : 7.96 % Favored : 90.04 % 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: -0.93 (0.20), residues: 1550 helix: -0.87 (0.16), residues: 908 sheet: 0.25 (0.38), residues: 150 loop : 0.05 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 823 TYR 0.021 0.002 TYR B 303 PHE 0.027 0.002 PHE A 87 TRP 0.016 0.002 TRP A 661 HIS 0.010 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (13330) covalent geometry : angle 0.72028 / 0.38 (18120) hydrogen bonds : bond 0.05961 / 3.84 ( 639) hydrogen bonds : angle 5.26799 / 3.71 ( 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 241 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.493 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 93 PHE cc_start: 0.7993 (m-80) cc_final: 0.7697 (m-80) REVERT: A 331 TYR cc_start: 0.8031 (t80) cc_final: 0.7620 (t80) REVERT: A 346 SER cc_start: 0.8395 (t) cc_final: 0.7901 (p) REVERT: A 391 MET cc_start: 0.7960 (mtp) cc_final: 0.7574 (mtt) REVERT: A 451 ASN cc_start: 0.6776 (p0) cc_final: 0.6552 (p0) REVERT: A 452 LEU cc_start: 0.8432 (mp) cc_final: 0.8212 (mt) REVERT: A 491 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: B 126 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7513 (mp0) REVERT: B 267 THR cc_start: 0.8437 (m) cc_final: 0.8201 (p) REVERT: B 316 MET cc_start: 0.6217 (mtm) cc_final: 0.5973 (mpp) REVERT: B 563 MET cc_start: 0.6902 (mtp) cc_final: 0.6656 (mtm) REVERT: B 587 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6521 (tpp) REVERT: B 634 ASP cc_start: 0.7625 (m-30) cc_final: 0.7296 (m-30) REVERT: B 738 ASN cc_start: 0.8083 (m-40) cc_final: 0.7707 (m-40) REVERT: B 843 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6659 (ttp-110) outliers start: 27 outliers final: 15 residues processed: 230 average time/residue: 0.1316 time to fit residues: 42.9342 Evaluate side-chains 186 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 455 ARG 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: 7.9990 chunk 113 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 366 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139418 restraints weight = 18479.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138262 restraints weight = 22420.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139725 restraints weight = 21354.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138464 restraints weight = 16152.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138889 restraints weight = 16429.662| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13330 Z= 0.214 Angle : 0.709 13.568 18120 Z= 0.371 Chirality : 0.045 0.252 2130 Planarity : 0.005 0.093 2161 Dihedral : 15.031 151.500 2122 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 10.32 % Favored : 86.87 % 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: -0.76 (0.20), residues: 1550 helix: -0.61 (0.16), residues: 906 sheet: -0.16 (0.36), residues: 160 loop : 0.04 (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 0.041 0.002 PHE B 87 TRP 0.015 0.002 TRP A 588 HIS 0.007 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (13330) covalent geometry : angle 0.70871 / 0.37 (18120) hydrogen bonds : bond 0.05242 / 3.32 ( 639) hydrogen bonds : angle 4.92298 / 3.47 ( 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 211 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.604 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: 0.7528 (t80) cc_final: 0.7259 (t80) REVERT: A 346 SER cc_start: 0.8492 (t) cc_final: 0.7946 (p) REVERT: A 718 ARG cc_start: 0.7624 (ttt180) cc_final: 0.6534 (ttt90) REVERT: A 776 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8072 (tt) REVERT: B 185 ASP cc_start: 0.7802 (m-30) cc_final: 0.7536 (m-30) REVERT: B 267 THR cc_start: 0.8465 (m) cc_final: 0.8173 (p) REVERT: B 563 MET cc_start: 0.6977 (mtp) cc_final: 0.6718 (mtm) REVERT: B 587 MET cc_start: 0.6878 (tpp) cc_final: 0.6614 (tpp) REVERT: B 738 ASN cc_start: 0.7978 (m-40) cc_final: 0.7593 (m-40) REVERT: B 843 ARG cc_start: 0.7205 (mtp85) cc_final: 0.6634 (ttp-110) outliers start: 38 outliers final: 23 residues processed: 198 average time/residue: 0.1301 time to fit residues: 36.7864 Evaluate side-chains 182 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 455 ARG 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 279 ASN 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 701 LYS 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: 4.9990 chunk 140 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.178487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140310 restraints weight = 18247.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139166 restraints weight = 22679.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140160 restraints weight = 21329.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139301 restraints weight = 18813.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139721 restraints weight = 16115.883| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13330 Z= 0.162 Angle : 0.643 12.298 18120 Z= 0.337 Chirality : 0.043 0.281 2130 Planarity : 0.004 0.038 2161 Dihedral : 14.917 150.546 2122 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 11.58 % Favored : 85.99 % 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: -0.49 (0.20), residues: 1550 helix: -0.33 (0.17), residues: 908 sheet: -0.13 (0.37), residues: 160 loop : 0.04 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 395 TYR 0.015 0.001 TYR B 303 PHE 0.012 0.001 PHE B 839 TRP 0.012 0.001 TRP A 588 HIS 0.007 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13330) covalent geometry : angle 0.64348 / 0.34 (18120) hydrogen bonds : bond 0.04519 / 2.87 ( 639) hydrogen bonds : angle 4.63653 / 3.28 ( 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 216 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.575 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 331 TYR cc_start: 0.7534 (t80) cc_final: 0.7273 (t80) REVERT: A 346 SER cc_start: 0.8430 (t) cc_final: 0.7884 (p) REVERT: A 718 ARG cc_start: 0.7588 (ttt180) cc_final: 0.6297 (tpt-90) REVERT: B 267 THR cc_start: 0.8403 (m) cc_final: 0.8076 (p) REVERT: B 401 LEU cc_start: 0.6800 (tp) cc_final: 0.6571 (tp) REVERT: B 563 MET cc_start: 0.6964 (mtp) cc_final: 0.6695 (mtm) REVERT: B 587 MET cc_start: 0.6902 (tpp) cc_final: 0.6578 (tpp) REVERT: B 731 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 738 ASN cc_start: 0.7915 (m-40) cc_final: 0.7540 (m-40) REVERT: B 843 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6770 (ttp-110) outliers start: 33 outliers final: 22 residues processed: 205 average time/residue: 0.1347 time to fit residues: 38.9547 Evaluate side-chains 183 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 241 THR 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 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 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 701 LYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 0.1980 chunk 159 optimal weight: 6.9990 chunk 38 optimal weight: 0.0060 chunk 108 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS A 451 ASN A 596 GLN A 752 GLN B 85 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.180987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142458 restraints weight = 18582.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141721 restraints weight = 21080.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143115 restraints weight = 19082.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142660 restraints weight = 15111.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142876 restraints weight = 15311.572| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13330 Z= 0.127 Angle : 0.624 12.804 18120 Z= 0.324 Chirality : 0.042 0.267 2130 Planarity : 0.004 0.034 2161 Dihedral : 14.834 149.538 2122 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.14 % Allowed : 13.42 % Favored : 84.44 % 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: 0.01 (0.17), residues: 906 sheet: -0.12 (0.37), residues: 160 loop : 0.06 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 395 TYR 0.012 0.001 TYR B 113 PHE 0.013 0.001 PHE A 432 TRP 0.014 0.001 TRP A 666 HIS 0.010 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13330) covalent geometry : angle 0.62386 / 0.32 (18120) hydrogen bonds : bond 0.04035 / 2.57 ( 639) hydrogen bonds : angle 4.42288 / 3.13 ( 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 209 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.494 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: 0.7644 (t80) cc_final: 0.7422 (t80) REVERT: A 346 SER cc_start: 0.8376 (t) cc_final: 0.7852 (p) REVERT: A 718 ARG cc_start: 0.7506 (ttt180) cc_final: 0.6370 (tpt-90) REVERT: A 776 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 401 LEU cc_start: 0.6523 (tp) cc_final: 0.6268 (tp) REVERT: B 587 MET cc_start: 0.6885 (tpp) cc_final: 0.6521 (tpp) REVERT: B 665 ASP cc_start: 0.6931 (p0) cc_final: 0.6702 (p0) REVERT: B 731 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 738 ASN cc_start: 0.7879 (m-40) cc_final: 0.7506 (m-40) REVERT: B 843 ARG cc_start: 0.7189 (mtp85) cc_final: 0.6762 (ttp-110) outliers start: 29 outliers final: 15 residues processed: 197 average time/residue: 0.1295 time to fit residues: 36.2741 Evaluate side-chains 171 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 362 TYR 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 325 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 701 LYS 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: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 551 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.178745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135981 restraints weight = 18471.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135373 restraints weight = 22548.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136690 restraints weight = 18224.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136400 restraints weight = 15570.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136614 restraints weight = 14495.192| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13330 Z= 0.170 Angle : 0.634 12.450 18120 Z= 0.328 Chirality : 0.043 0.266 2130 Planarity : 0.004 0.037 2161 Dihedral : 14.861 148.825 2122 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 13.64 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1550 helix: 0.08 (0.17), residues: 902 sheet: -0.52 (0.39), residues: 142 loop : 0.08 (0.27), residues: 506 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 0.014 0.002 PHE A 432 TRP 0.013 0.001 TRP A 95 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13330) covalent geometry : angle 0.63443 / 0.33 (18120) hydrogen bonds : bond 0.04134 / 2.62 ( 639) hydrogen bonds : angle 4.43715 / 3.15 ( 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 197 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.486 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 331 TYR cc_start: 0.8000 (t80) cc_final: 0.7775 (t80) REVERT: A 346 SER cc_start: 0.8391 (t) cc_final: 0.7803 (p) REVERT: A 718 ARG cc_start: 0.7642 (ttt180) cc_final: 0.6533 (tpt-90) REVERT: A 758 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: B 185 ASP cc_start: 0.7717 (m-30) cc_final: 0.7396 (m-30) REVERT: B 587 MET cc_start: 0.6959 (tpp) cc_final: 0.6621 (tpp) REVERT: B 738 ASN cc_start: 0.7903 (m-40) cc_final: 0.7570 (m-40) REVERT: B 806 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7070 (mtp85) REVERT: B 843 ARG cc_start: 0.7217 (mtp85) cc_final: 0.6765 (ttp-110) outliers start: 29 outliers final: 20 residues processed: 185 average time/residue: 0.1215 time to fit residues: 32.6203 Evaluate side-chains 181 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 362 TYR Chi-restraints excluded: chain A residue 427 ILE 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 B residue 71 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 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 701 LYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR 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: 10.0000 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4209 r_free = 0.4209 target = 0.178605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138895 restraints weight = 18406.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137603 restraints weight = 23677.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139082 restraints weight = 20228.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138937 restraints weight = 16963.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139108 restraints weight = 16016.197| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4112 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= 0.166 Angle : 0.649 15.205 18120 Z= 0.332 Chirality : 0.043 0.312 2130 Planarity : 0.004 0.039 2161 Dihedral : 14.876 147.894 2122 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.36 % Allowed : 14.38 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.21), residues: 1550 helix: 0.16 (0.17), residues: 912 sheet: -0.22 (0.39), residues: 150 loop : 0.01 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 884 TYR 0.010 0.001 TYR B 303 PHE 0.015 0.002 PHE A 432 TRP 0.013 0.001 TRP A 95 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13330) covalent geometry : angle 0.64947 / 0.33 (18120) hydrogen bonds : bond 0.04055 / 2.56 ( 639) hydrogen bonds : angle 4.39654 / 3.13 ( 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 204 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.507 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: 0.7636 (t80) cc_final: 0.7326 (t80) REVERT: A 346 SER cc_start: 0.8353 (t) cc_final: 0.7743 (p) REVERT: A 718 ARG cc_start: 0.7609 (ttt180) cc_final: 0.6357 (tpt-90) REVERT: A 776 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 537 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6363 (mt-10) REVERT: B 587 MET cc_start: 0.6951 (tpp) cc_final: 0.6643 (tpp) REVERT: B 738 ASN cc_start: 0.7884 (m-40) cc_final: 0.7545 (m-40) REVERT: B 806 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6653 (mtp85) REVERT: B 843 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6773 (ttp-110) outliers start: 32 outliers final: 24 residues processed: 189 average time/residue: 0.1230 time to fit residues: 33.6471 Evaluate side-chains 190 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 427 ILE Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 654 VAL 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 71 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 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 758 TYR 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: 0.0010 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4228 r_free = 0.4228 target = 0.180321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140577 restraints weight = 18406.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140156 restraints weight = 21679.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139612 restraints weight = 17578.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138743 restraints weight = 18441.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139687 restraints weight = 15832.655| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13330 Z= 0.128 Angle : 0.618 13.312 18120 Z= 0.318 Chirality : 0.042 0.434 2130 Planarity : 0.004 0.040 2161 Dihedral : 14.803 147.175 2122 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 14.68 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.21), residues: 1550 helix: 0.31 (0.17), residues: 910 sheet: -0.14 (0.39), residues: 150 loop : 0.02 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 395 TYR 0.010 0.001 TYR B 113 PHE 0.021 0.001 PHE A 432 TRP 0.022 0.001 TRP A 863 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13330) covalent geometry : angle 0.61814 / 0.32 (18120) hydrogen bonds : bond 0.03807 / 2.41 ( 639) hydrogen bonds : angle 4.31679 / 3.06 ( 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 200 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.483 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 346 SER cc_start: 0.8256 (t) cc_final: 0.7714 (p) REVERT: A 391 MET cc_start: 0.5670 (mtt) cc_final: 0.5373 (mtt) REVERT: A 718 ARG cc_start: 0.7518 (ttt180) cc_final: 0.6340 (tpt-90) REVERT: A 776 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8185 (tt) REVERT: B 587 MET cc_start: 0.6923 (tpp) cc_final: 0.6603 (tpp) REVERT: B 738 ASN cc_start: 0.7829 (m-40) cc_final: 0.7493 (m-40) REVERT: B 806 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6688 (mtp85) REVERT: B 843 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6773 (ttp-110) outliers start: 28 outliers final: 23 residues processed: 188 average time/residue: 0.1292 time to fit residues: 34.7674 Evaluate side-chains 191 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR 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 71 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 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 835 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142498 restraints weight = 18644.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141166 restraints weight = 23300.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141891 restraints weight = 21665.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140058 restraints weight = 19892.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140594 restraints weight = 18246.238| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13330 Z= 0.130 Angle : 0.633 12.805 18120 Z= 0.322 Chirality : 0.044 0.680 2130 Planarity : 0.004 0.039 2161 Dihedral : 14.743 146.397 2122 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.06 % Allowed : 14.45 % Favored : 83.48 % 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: 0.21 (0.21), residues: 1550 helix: 0.39 (0.17), residues: 910 sheet: -0.05 (0.39), residues: 150 loop : 0.03 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 395 TYR 0.067 0.001 TYR A 331 PHE 0.024 0.001 PHE A 432 TRP 0.014 0.001 TRP A 95 HIS 0.008 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13330) covalent geometry : angle 0.63254 / 0.32 (18120) hydrogen bonds : bond 0.03782 / 2.40 ( 639) hydrogen bonds : angle 4.28772 / 3.05 ( 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 199 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.543 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: A 212 MET cc_start: 0.7472 (ttm) cc_final: 0.7085 (ttt) REVERT: A 346 SER cc_start: 0.8245 (t) cc_final: 0.7773 (p) REVERT: A 718 ARG cc_start: 0.7492 (ttt180) cc_final: 0.6313 (tpt-90) REVERT: A 776 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 587 MET cc_start: 0.6928 (tpp) cc_final: 0.6599 (tpp) REVERT: B 738 ASN cc_start: 0.7816 (m-40) cc_final: 0.7471 (m-40) REVERT: B 806 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6702 (mtp85) REVERT: B 843 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6760 (ttp-110) outliers start: 28 outliers final: 22 residues processed: 188 average time/residue: 0.1243 time to fit residues: 33.7446 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 : 0.496 ------------------------------------------------------------------------------- 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 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 619 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR 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 71 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 175 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 758 TYR Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 806 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 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 = 0.4230 r_free = 0.4230 target = 0.180455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143396 restraints weight = 18670.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142396 restraints weight = 22096.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142635 restraints weight = 21378.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141553 restraints weight = 19877.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142010 restraints weight = 18533.417| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13330 Z= 0.138 Angle : 0.655 12.965 18120 Z= 0.329 Chirality : 0.044 0.662 2130 Planarity : 0.004 0.100 2161 Dihedral : 14.720 145.779 2122 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.92 % Allowed : 14.90 % Favored : 83.19 % 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: 0.19 (0.21), residues: 1550 helix: 0.36 (0.17), residues: 908 sheet: -0.06 (0.39), residues: 150 loop : 0.05 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 395 TYR 0.020 0.001 TYR A 331 PHE 0.022 0.001 PHE A 432 TRP 0.014 0.001 TRP A 95 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13330) covalent geometry : angle 0.65505 / 0.33 (18120) hydrogen bonds : bond 0.03796 / 2.39 ( 639) hydrogen bonds : angle 4.30593 / 3.07 ( 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 194 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.424 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: A 212 MET cc_start: 0.7500 (ttm) cc_final: 0.7127 (ttt) REVERT: A 346 SER cc_start: 0.8088 (t) cc_final: 0.7629 (p) REVERT: A 718 ARG cc_start: 0.7466 (ttt180) cc_final: 0.6259 (tpt-90) REVERT: A 776 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 587 MET cc_start: 0.6928 (tpp) cc_final: 0.6608 (tpp) REVERT: B 738 ASN cc_start: 0.7801 (m-40) cc_final: 0.7490 (m-40) REVERT: B 806 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6682 (mtp85) REVERT: B 843 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6774 (ttp-110) outliers start: 26 outliers final: 20 residues processed: 185 average time/residue: 0.1248 time to fit residues: 33.1586 Evaluate side-chains 181 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR 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 71 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 175 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 758 TYR Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 806 ARG 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: 0.6980 chunk 65 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS A 451 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142627 restraints weight = 18519.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141781 restraints weight = 22584.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142945 restraints weight = 20656.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143105 restraints weight = 17589.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143231 restraints weight = 16439.749| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13330 Z= 0.137 Angle : 0.648 12.693 18120 Z= 0.327 Chirality : 0.043 0.464 2130 Planarity : 0.004 0.047 2161 Dihedral : 14.676 144.713 2122 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 14.90 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1550 helix: 0.41 (0.17), residues: 908 sheet: -0.03 (0.39), residues: 150 loop : 0.02 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 395 TYR 0.015 0.001 TYR B 239 PHE 0.023 0.001 PHE A 432 TRP 0.014 0.001 TRP A 95 HIS 0.006 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13330) covalent geometry : angle 0.64817 / 0.33 (18120) hydrogen bonds : bond 0.03760 / 2.38 ( 639) hydrogen bonds : angle 4.29933 / 3.06 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.95 seconds wall clock time: 40 minutes 19.75 seconds (2419.75 seconds total)