Starting phenix.real_space_refine on Sat Aug 23 15:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh8_44536/08_2025/9bh8_44536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh8_44536/08_2025/9bh8_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_44536/08_2025/9bh8_44536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2025/9bh8_44536.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2025/9bh8_44536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh8_44536/08_2025/9bh8_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13051 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 215 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3} Unresolved non-hydrogen planarities: 58 Chain: "Y" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 430 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1, ' DT:plan': 12, ' DG:plan': 5, ' DG:plan2': 5, ' DA:plan': 2, ' DA:plan2': 2, ' DC:plan': 2, ' DC:plan2': 2} Unresolved non-hydrogen planarities: 227 Time building chain proxies: 2.95, per 1000 atoms: 0.23 Number of scatterers: 13051 At special positions: 0 Unit cell: (125.783, 149.94, 89.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 43 15.00 O 2491 8.00 N 2210 7.00 C 8229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 442.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.41 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: 2.19 Time building geometry restraints manager: 1.10 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=" C4' DT Y 39 " pdb=" O4' DT Y 39 " ideal model delta sigma weight residual 1.450 1.412 0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" O4' DG Y 41 " pdb=" C1' DG Y 41 " ideal model delta sigma weight residual 1.414 1.379 0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C4' DT X 48 " pdb=" O4' DT X 48 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C3' DT X 48 " pdb=" C2' DT X 48 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " ideal model delta sigma weight residual 1.450 1.421 0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 13325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17289 1.39 - 2.78: 714 2.78 - 4.17: 98 4.17 - 5.56: 17 5.56 - 6.95: 2 Bond angle restraints: 18120 Sorted by residual: angle pdb=" C5' DG X 50 " pdb=" C4' DG X 50 " pdb=" C3' DG X 50 " ideal model delta sigma weight residual 114.90 119.72 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C5' DG Y 41 " pdb=" C4' DG Y 41 " pdb=" C3' DG Y 41 " ideal model delta sigma weight residual 114.90 119.61 -4.71 1.50e+00 4.44e-01 9.86e+00 angle pdb=" O4' DA Y 29 " pdb=" C1' DA Y 29 " pdb=" C2' DA Y 29 " ideal model delta sigma weight residual 106.40 101.93 4.47 1.50e+00 4.44e-01 8.86e+00 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 109.70 105.55 4.15 1.50e+00 4.44e-01 7.65e+00 angle pdb=" C4' DC X 53 " pdb=" O4' DC X 53 " pdb=" C1' DC X 53 " ideal model delta sigma weight residual 109.70 105.66 4.04 1.50e+00 4.44e-01 7.27e+00 ... (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 - 0.050: 1682 0.050 - 0.100: 358 0.100 - 0.150: 84 0.150 - 0.200: 3 0.200 - 0.250: 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 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C3' DG X 50 " pdb=" C4' DG X 50 " pdb=" O3' DG X 50 " pdb=" C2' DG X 50 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.28e+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 -0.20 2.00e-01 2.50e+01 1.01e+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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 0.039 13330 Z= 0.139 Angle : 0.641 6.951 18120 Z= 0.384 Chirality : 0.044 0.250 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 aren 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 covalent geometry : bond 0.00302 (13330) covalent geometry : angle 0.64092 (18120) hydrogen bonds : bond 0.20833 ( 639) hydrogen bonds : angle 7.98511 ( 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 : 0.360 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: 0.1269 time to fit residues: 55.0966 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 : 0.398 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 279 ASN A 300 ASN A 337 ASN A 592 ASN A 710 HIS A 816 HIS B 73 ASN B 195 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 738 ASN B 816 HIS B 825 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138754 restraints weight = 18240.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138049 restraints weight = 23058.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140469 restraints weight = 19043.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139980 restraints weight = 14374.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140018 restraints weight = 15087.757| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13330 Z= 0.170 Angle : 0.664 9.829 18120 Z= 0.350 Chirality : 0.043 0.152 2130 Planarity : 0.004 0.043 2161 Dihedral : 14.813 149.287 2122 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.06 % Allowed : 8.26 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.20), residues: 1550 helix: -0.58 (0.16), residues: 904 sheet: 0.05 (0.37), residues: 160 loop : 0.07 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 433 TYR 0.026 0.002 TYR B 303 PHE 0.032 0.002 PHE A 87 TRP 0.015 0.002 TRP A 661 HIS 0.010 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00392 (13330) covalent geometry : angle 0.66410 (18120) hydrogen bonds : bond 0.05075 ( 639) hydrogen bonds : angle 4.91238 ( 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 236 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.333 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: 0.7721 (t80) cc_final: 0.7378 (t80) REVERT: A 346 SER cc_start: 0.8495 (t) cc_final: 0.7973 (p) REVERT: A 471 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 491 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: B 267 THR cc_start: 0.8409 (m) cc_final: 0.8097 (p) REVERT: B 563 MET cc_start: 0.6930 (mtp) cc_final: 0.6675 (mtm) REVERT: B 587 MET cc_start: 0.6870 (tpp) cc_final: 0.6587 (tpp) REVERT: B 634 ASP cc_start: 0.7527 (m-30) cc_final: 0.7194 (m-30) REVERT: B 738 ASN cc_start: 0.8050 (m-40) cc_final: 0.7706 (m-40) REVERT: B 843 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6545 (ttp-110) outliers start: 28 outliers final: 13 residues processed: 227 average time/residue: 0.1133 time to fit residues: 35.6701 Evaluate side-chains 181 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 237 ILE 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 758 TYR 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 660 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 366 HIS A 752 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 325 HIS B 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.180414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137952 restraints weight = 18089.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137527 restraints weight = 17612.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137930 restraints weight = 16582.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138858 restraints weight = 14153.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139062 restraints weight = 12897.496| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13330 Z= 0.134 Angle : 0.594 8.907 18120 Z= 0.313 Chirality : 0.040 0.156 2130 Planarity : 0.004 0.039 2161 Dihedral : 14.485 145.740 2122 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.36 % Allowed : 9.51 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.20), residues: 1550 helix: -0.02 (0.17), residues: 906 sheet: 0.08 (0.37), residues: 160 loop : 0.13 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 359 TYR 0.017 0.001 TYR B 303 PHE 0.012 0.001 PHE A 422 TRP 0.013 0.001 TRP A 588 HIS 0.006 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00298 (13330) covalent geometry : angle 0.59369 (18120) hydrogen bonds : bond 0.04120 ( 639) hydrogen bonds : angle 4.44102 ( 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 224 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.336 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: 0.7913 (t80) cc_final: 0.7585 (t80) REVERT: A 346 SER cc_start: 0.8333 (t) cc_final: 0.7810 (p) REVERT: A 537 GLU cc_start: 0.6202 (tm-30) cc_final: 0.5853 (tp30) REVERT: A 619 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 718 ARG cc_start: 0.7380 (ttt180) cc_final: 0.6313 (tpt-90) REVERT: B 157 LEU cc_start: 0.8222 (mt) cc_final: 0.8014 (mt) REVERT: B 212 MET cc_start: 0.7853 (ttm) cc_final: 0.7647 (ttm) REVERT: B 267 THR cc_start: 0.8350 (m) cc_final: 0.8036 (p) REVERT: B 279 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7440 (t0) REVERT: B 587 MET cc_start: 0.6956 (tpp) cc_final: 0.6533 (tpp) REVERT: B 634 ASP cc_start: 0.7941 (m-30) cc_final: 0.7644 (m-30) REVERT: B 738 ASN cc_start: 0.7961 (m-40) cc_final: 0.7647 (m-40) REVERT: B 843 ARG cc_start: 0.7156 (mtp85) cc_final: 0.6629 (ttp-110) outliers start: 32 outliers final: 16 residues processed: 212 average time/residue: 0.1054 time to fit residues: 31.3340 Evaluate side-chains 187 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 619 LEU 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 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 687 VAL Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 884 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 85 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 551 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138008 restraints weight = 18415.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136206 restraints weight = 20863.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137275 restraints weight = 19983.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138013 restraints weight = 16848.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138080 restraints weight = 15424.880| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13330 Z= 0.143 Angle : 0.589 10.033 18120 Z= 0.307 Chirality : 0.040 0.151 2130 Planarity : 0.004 0.035 2161 Dihedral : 14.401 143.226 2122 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.14 % Allowed : 11.36 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1550 helix: 0.15 (0.17), residues: 910 sheet: -0.17 (0.40), residues: 142 loop : 0.14 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.013 0.001 TYR B 303 PHE 0.012 0.001 PHE A 670 TRP 0.011 0.001 TRP A 588 HIS 0.014 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00333 (13330) covalent geometry : angle 0.58887 (18120) hydrogen bonds : bond 0.03890 ( 639) hydrogen bonds : angle 4.29974 ( 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 209 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.7845 (t80) cc_final: 0.7603 (t80) REVERT: A 346 SER cc_start: 0.8347 (t) cc_final: 0.7828 (p) REVERT: A 391 MET cc_start: 0.5871 (mtt) cc_final: 0.5182 (mtt) REVERT: A 392 ASP cc_start: 0.7497 (t0) cc_final: 0.7134 (t0) REVERT: A 718 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6379 (tpt-90) REVERT: A 776 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (tt) REVERT: B 157 LEU cc_start: 0.8129 (mt) cc_final: 0.7851 (mt) REVERT: B 267 THR cc_start: 0.8318 (m) cc_final: 0.8051 (p) REVERT: B 587 MET cc_start: 0.6945 (tpp) cc_final: 0.6580 (tpp) REVERT: B 634 ASP cc_start: 0.8073 (m-30) cc_final: 0.7724 (m-30) REVERT: B 738 ASN cc_start: 0.7933 (m-40) cc_final: 0.7602 (m-40) REVERT: B 843 ARG cc_start: 0.7257 (mtp85) cc_final: 0.6791 (ttp-110) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 0.1029 time to fit residues: 28.6983 Evaluate side-chains 183 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 427 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 654 VAL 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 324 ASP 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 660 ASP 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: 0.9980 chunk 111 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 114 optimal weight: 0.0030 chunk 159 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 752 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.178136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135825 restraints weight = 18259.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134893 restraints weight = 18919.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136479 restraints weight = 17168.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136910 restraints weight = 13568.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136936 restraints weight = 13435.139| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4101 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= 0.161 Angle : 0.599 11.570 18120 Z= 0.311 Chirality : 0.041 0.197 2130 Planarity : 0.004 0.036 2161 Dihedral : 14.419 141.508 2122 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.29 % Allowed : 12.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.21), residues: 1550 helix: 0.24 (0.17), residues: 916 sheet: -0.04 (0.38), residues: 160 loop : 0.14 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 395 TYR 0.012 0.001 TYR B 303 PHE 0.018 0.001 PHE B 670 TRP 0.013 0.001 TRP A 863 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00379 (13330) covalent geometry : angle 0.59890 (18120) hydrogen bonds : bond 0.03909 ( 639) hydrogen bonds : angle 4.31963 ( 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 206 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.357 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: 0.7920 (t80) cc_final: 0.7623 (t80) REVERT: A 346 SER cc_start: 0.8297 (t) cc_final: 0.7776 (p) REVERT: A 718 ARG cc_start: 0.7562 (ttt180) cc_final: 0.6437 (tpt-90) REVERT: A 776 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8201 (tt) REVERT: B 185 ASP cc_start: 0.7785 (m-30) cc_final: 0.7471 (m-30) REVERT: B 587 MET cc_start: 0.6981 (tpp) cc_final: 0.6598 (tpp) REVERT: B 634 ASP cc_start: 0.8138 (m-30) cc_final: 0.7780 (m-30) REVERT: B 738 ASN cc_start: 0.7960 (m-40) cc_final: 0.7648 (m-40) REVERT: B 834 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8200 (tttm) REVERT: B 843 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6750 (ttp-110) outliers start: 31 outliers final: 23 residues processed: 195 average time/residue: 0.0953 time to fit residues: 26.8864 Evaluate side-chains 187 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 427 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 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 829 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4172 r_free = 0.4172 target = 0.176507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134099 restraints weight = 18192.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132898 restraints weight = 18824.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134466 restraints weight = 17412.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135035 restraints weight = 13711.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135237 restraints weight = 12932.407| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13330 Z= 0.167 Angle : 0.605 11.799 18120 Z= 0.313 Chirality : 0.041 0.201 2130 Planarity : 0.004 0.044 2161 Dihedral : 14.436 139.834 2122 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.29 % Allowed : 13.13 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1550 helix: 0.24 (0.17), residues: 920 sheet: -0.04 (0.39), residues: 150 loop : 0.04 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 396 TYR 0.011 0.001 TYR A 113 PHE 0.015 0.002 PHE B 670 TRP 0.011 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00398 (13330) covalent geometry : angle 0.60475 (18120) hydrogen bonds : bond 0.03899 ( 639) hydrogen bonds : angle 4.33033 ( 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 202 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.492 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 212 MET cc_start: 0.7683 (ttm) cc_final: 0.7375 (ttm) REVERT: A 331 TYR cc_start: 0.7929 (t80) cc_final: 0.7683 (t80) REVERT: A 346 SER cc_start: 0.8273 (t) cc_final: 0.7849 (p) REVERT: A 392 ASP cc_start: 0.7588 (t0) cc_final: 0.7357 (t0) REVERT: A 395 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7751 (mtm-85) REVERT: A 718 ARG cc_start: 0.7603 (ttt180) cc_final: 0.6435 (tpt-90) REVERT: A 776 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 185 ASP cc_start: 0.7814 (m-30) cc_final: 0.7449 (m-30) REVERT: B 537 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6415 (mt-10) REVERT: B 587 MET cc_start: 0.6964 (tpp) cc_final: 0.6594 (tpp) REVERT: B 634 ASP cc_start: 0.8089 (m-30) cc_final: 0.7711 (m-30) REVERT: B 738 ASN cc_start: 0.7942 (m-40) cc_final: 0.7638 (m-40) REVERT: B 806 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6771 (mtp85) REVERT: B 833 LEU cc_start: 0.7978 (mp) cc_final: 0.7581 (mp) REVERT: B 834 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8114 (tttm) REVERT: B 843 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6760 (ttp-110) outliers start: 31 outliers final: 22 residues processed: 191 average time/residue: 0.1043 time to fit residues: 28.3303 Evaluate side-chains 187 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 317 LEU 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 Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4198 r_free = 0.4198 target = 0.178976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136608 restraints weight = 18057.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136077 restraints weight = 18369.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137399 restraints weight = 16394.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137971 restraints weight = 13601.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138105 restraints weight = 12797.071| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13330 Z= 0.125 Angle : 0.578 10.249 18120 Z= 0.299 Chirality : 0.040 0.233 2130 Planarity : 0.004 0.040 2161 Dihedral : 14.243 137.654 2122 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.14 % Allowed : 14.23 % Favored : 83.63 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1550 helix: 0.49 (0.17), residues: 908 sheet: 0.10 (0.39), residues: 154 loop : 0.06 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 396 TYR 0.012 0.001 TYR B 113 PHE 0.020 0.001 PHE A 432 TRP 0.011 0.001 TRP B 95 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00286 (13330) covalent geometry : angle 0.57795 (18120) hydrogen bonds : bond 0.03505 ( 639) hydrogen bonds : angle 4.17621 ( 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 201 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.375 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 346 SER cc_start: 0.8027 (t) cc_final: 0.7574 (p) REVERT: A 452 LEU cc_start: 0.8274 (mm) cc_final: 0.8009 (mt) REVERT: A 718 ARG cc_start: 0.7534 (ttt180) cc_final: 0.6363 (tpt-90) REVERT: B 239 TYR cc_start: 0.7813 (t80) cc_final: 0.7597 (t80) REVERT: B 537 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6467 (mt-10) REVERT: B 583 GLU cc_start: 0.7817 (pm20) cc_final: 0.7515 (pm20) REVERT: B 587 MET cc_start: 0.6926 (tpp) cc_final: 0.6548 (tpp) REVERT: B 634 ASP cc_start: 0.8052 (m-30) cc_final: 0.7664 (m-30) REVERT: B 738 ASN cc_start: 0.7834 (m-40) cc_final: 0.7503 (m-40) REVERT: B 806 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6644 (mtp85) REVERT: B 834 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8050 (tttm) REVERT: B 843 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6788 (ttp-110) outliers start: 29 outliers final: 21 residues processed: 190 average time/residue: 0.0967 time to fit residues: 26.7251 Evaluate side-chains 184 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 350 CYS 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 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 317 LEU 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: 0.1980 chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 28 optimal weight: 9.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4216 r_free = 0.4216 target = 0.180591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137985 restraints weight = 18045.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135600 restraints weight = 16793.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136424 restraints weight = 15236.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137186 restraints weight = 13517.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137440 restraints weight = 12142.000| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13330 Z= 0.114 Angle : 0.612 15.135 18120 Z= 0.306 Chirality : 0.040 0.441 2130 Planarity : 0.004 0.039 2161 Dihedral : 14.175 138.958 2122 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.06 % Allowed : 14.38 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.21), residues: 1550 helix: 0.62 (0.17), residues: 908 sheet: 0.37 (0.39), residues: 154 loop : 0.02 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 884 TYR 0.050 0.001 TYR A 331 PHE 0.020 0.001 PHE A 432 TRP 0.012 0.001 TRP A 588 HIS 0.003 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00253 (13330) covalent geometry : angle 0.61224 (18120) hydrogen bonds : bond 0.03352 ( 639) hydrogen bonds : angle 4.09397 ( 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 204 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.377 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 295 SER cc_start: 0.7231 (p) cc_final: 0.6936 (m) REVERT: A 346 SER cc_start: 0.7923 (t) cc_final: 0.7423 (p) REVERT: A 391 MET cc_start: 0.6558 (mmt) cc_final: 0.5545 (mmt) REVERT: A 452 LEU cc_start: 0.8283 (mm) cc_final: 0.8022 (mt) REVERT: A 718 ARG cc_start: 0.7483 (ttt180) cc_final: 0.6300 (tpt-90) REVERT: B 537 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6469 (mt-10) REVERT: B 583 GLU cc_start: 0.7781 (pm20) cc_final: 0.7338 (pm20) REVERT: B 587 MET cc_start: 0.6956 (tpp) cc_final: 0.6526 (tpp) REVERT: B 634 ASP cc_start: 0.7969 (m-30) cc_final: 0.7568 (m-30) REVERT: B 738 ASN cc_start: 0.7792 (m-40) cc_final: 0.7473 (m-40) REVERT: B 806 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6580 (mtp85) REVERT: B 834 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7966 (tttm) REVERT: B 843 ARG cc_start: 0.7329 (mtp85) cc_final: 0.6771 (ttp-110) outliers start: 28 outliers final: 21 residues processed: 196 average time/residue: 0.0918 time to fit residues: 26.1588 Evaluate side-chains 184 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 350 CYS 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 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 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL 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: 0.8980 chunk 7 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 114 optimal weight: 0.3980 chunk 121 optimal weight: 0.0060 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4218 r_free = 0.4218 target = 0.180825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137642 restraints weight = 18284.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136051 restraints weight = 17840.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138487 restraints weight = 15070.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138856 restraints weight = 12407.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138809 restraints weight = 11788.465| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13330 Z= 0.114 Angle : 0.612 14.644 18120 Z= 0.306 Chirality : 0.040 0.306 2130 Planarity : 0.004 0.089 2161 Dihedral : 14.150 139.741 2122 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 14.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1550 helix: 0.75 (0.17), residues: 906 sheet: 0.58 (0.39), residues: 154 loop : 0.14 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 395 TYR 0.010 0.001 TYR B 113 PHE 0.021 0.001 PHE A 432 TRP 0.017 0.001 TRP A 95 HIS 0.003 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00254 (13330) covalent geometry : angle 0.61223 (18120) hydrogen bonds : bond 0.03287 ( 639) hydrogen bonds : angle 4.07243 ( 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 204 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.353 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 295 SER cc_start: 0.7309 (p) cc_final: 0.6990 (m) REVERT: A 346 SER cc_start: 0.7902 (t) cc_final: 0.7349 (p) REVERT: A 473 THR cc_start: 0.8478 (m) cc_final: 0.8255 (t) REVERT: A 718 ARG cc_start: 0.7479 (ttt180) cc_final: 0.6354 (tpt-90) REVERT: B 537 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6449 (mt-10) REVERT: B 583 GLU cc_start: 0.7767 (pm20) cc_final: 0.7323 (pm20) REVERT: B 587 MET cc_start: 0.6949 (tpp) cc_final: 0.6516 (tpp) REVERT: B 634 ASP cc_start: 0.7922 (m-30) cc_final: 0.7526 (m-30) REVERT: B 806 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6600 (mtp85) REVERT: B 834 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8068 (tttm) REVERT: B 843 ARG cc_start: 0.7320 (mtp85) cc_final: 0.6718 (ttp-110) outliers start: 25 outliers final: 21 residues processed: 198 average time/residue: 0.0948 time to fit residues: 27.7196 Evaluate side-chains 191 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 350 CYS 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 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 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4217 r_free = 0.4217 target = 0.180628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137137 restraints weight = 18346.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136825 restraints weight = 16957.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137826 restraints weight = 15622.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138784 restraints weight = 12961.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138671 restraints weight = 11987.172| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4961 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= 0.118 Angle : 0.631 14.397 18120 Z= 0.314 Chirality : 0.040 0.327 2130 Planarity : 0.004 0.064 2161 Dihedral : 14.155 139.797 2122 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.77 % Allowed : 15.12 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.21), residues: 1550 helix: 0.78 (0.17), residues: 906 sheet: 0.66 (0.39), residues: 154 loop : 0.11 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 395 TYR 0.041 0.001 TYR A 331 PHE 0.023 0.001 PHE B 161 TRP 0.016 0.001 TRP B 277 HIS 0.003 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00268 (13330) covalent geometry : angle 0.63065 (18120) hydrogen bonds : bond 0.03314 ( 639) hydrogen bonds : angle 4.09205 ( 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: 24 poor density : 170 time to evaluate : 0.314 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 295 SER cc_start: 0.7315 (p) cc_final: 0.7004 (m) REVERT: A 331 TYR cc_start: 0.8172 (t80) cc_final: 0.7960 (t80) REVERT: A 346 SER cc_start: 0.7896 (t) cc_final: 0.7310 (p) REVERT: A 473 THR cc_start: 0.8459 (m) cc_final: 0.8258 (t) REVERT: A 718 ARG cc_start: 0.7409 (ttt180) cc_final: 0.6284 (tpt-90) REVERT: B 316 MET cc_start: 0.6476 (pmm) cc_final: 0.6109 (pmm) REVERT: B 537 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6474 (mt-10) REVERT: B 583 GLU cc_start: 0.7761 (pm20) cc_final: 0.7335 (pm20) REVERT: B 587 MET cc_start: 0.6964 (tpp) cc_final: 0.6524 (tpp) REVERT: B 634 ASP cc_start: 0.7931 (m-30) cc_final: 0.7528 (m-30) REVERT: B 834 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7943 (tttm) REVERT: B 843 ARG cc_start: 0.7289 (mtp85) cc_final: 0.6672 (ttp-110) outliers start: 24 outliers final: 23 residues processed: 188 average time/residue: 0.0892 time to fit residues: 24.3870 Evaluate side-chains 189 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 350 CYS 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 753 GLN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 806 ARG Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 0.0980 chunk 65 optimal weight: 0.0980 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4211 r_free = 0.4211 target = 0.180077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138134 restraints weight = 18084.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136318 restraints weight = 20852.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137880 restraints weight = 18309.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138541 restraints weight = 15381.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138715 restraints weight = 13528.628| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13330 Z= 0.126 Angle : 0.620 14.140 18120 Z= 0.312 Chirality : 0.040 0.305 2130 Planarity : 0.004 0.068 2161 Dihedral : 14.205 139.951 2122 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 15.27 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1550 helix: 0.78 (0.17), residues: 904 sheet: 0.62 (0.40), residues: 154 loop : 0.11 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 884 TYR 0.036 0.001 TYR A 331 PHE 0.019 0.001 PHE A 432 TRP 0.016 0.001 TRP A 95 HIS 0.003 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00289 (13330) covalent geometry : angle 0.61951 (18120) hydrogen bonds : bond 0.03350 ( 639) hydrogen bonds : angle 4.09891 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.49 seconds wall clock time: 30 minutes 46.16 seconds (1846.16 seconds total)