Starting phenix.real_space_refine on Wed Jun 11 16:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh8_44536/06_2025/9bh8_44536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh8_44536/06_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_44536/06_2025/9bh8_44536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh8_44536/06_2025/9bh8_44536.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh8_44536/06_2025/9bh8_44536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh8_44536/06_2025/9bh8_44536.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3, ' DC:plan': 1, ' DT:plan': 1} 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: {' DG:plan': 5, ' DG:plan2': 5, ' DC:plan2': 2, ' DA:plan2': 2, ' DC%5*END:plan2': 1, ' DC:plan': 2, ' DC%5*END:plan': 1, ' DT:plan': 12, ' DA:plan': 2} Unresolved non-hydrogen planarities: 227 Time building chain proxies: 8.67, per 1000 atoms: 0.66 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.47 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: 4.53 Time building geometry restraints manager: 3.73 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.260 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP A 411 HIS 0.008 0.001 HIS A 366 PHE 0.022 0.001 PHE B 815 TYR 0.030 0.005 TYR B 553 ARG 0.020 0.003 ARG B 711 Details of bonding type rmsd hydrogen bonds : bond 0.20833 ( 639) hydrogen bonds : angle 7.98511 ( 1839) covalent geometry : bond 0.00302 (13330) covalent geometry : angle 0.64092 (18120) *********************** 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 : 1.330 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 122 THR cc_start: 0.7281 (p) cc_final: 0.6980 (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: 0.7674 (p) REVERT: A 619 LEU cc_start: 0.8307 (mp) cc_final: 0.7915 (mp) REVERT: A 639 MET cc_start: 0.9124 (mmm) cc_final: 0.8746 (mmt) REVERT: A 780 GLN cc_start: 0.7682 (tt0) cc_final: 0.7278 (tt0) REVERT: B 267 THR cc_start: 0.8514 (m) cc_final: 0.8311 (p) REVERT: B 563 MET cc_start: 0.7109 (mtp) cc_final: 0.6858 (mtm) REVERT: B 634 ASP cc_start: 0.7745 (m-30) cc_final: 0.7507 (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: 0.6727 (ttp-110) outliers start: 2 outliers final: 1 residues processed: 324 average time/residue: 0.3229 time to fit residues: 139.9167 Evaluate side-chains 202 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 135 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 279 ASN B 406 GLN B 738 ASN B 825 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136703 restraints weight = 18042.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137746 restraints weight = 18808.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139193 restraints weight = 15891.208| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13330 Z= 0.153 Angle : 0.653 10.319 18120 Z= 0.345 Chirality : 0.042 0.159 2130 Planarity : 0.004 0.034 2161 Dihedral : 14.778 149.224 2122 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.06 % Allowed : 8.19 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1550 helix: -0.49 (0.16), residues: 906 sheet: 0.13 (0.37), residues: 160 loop : 0.09 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 661 HIS 0.010 0.001 HIS B 85 PHE 0.031 0.002 PHE A 87 TYR 0.023 0.002 TYR B 303 ARG 0.005 0.001 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 639) hydrogen bonds : angle 4.80937 ( 1839) covalent geometry : bond 0.00343 (13330) covalent geometry : angle 0.65328 (18120) *********************** 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 244 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.435 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 93 PHE cc_start: 0.8058 (m-80) cc_final: 0.7706 (m-80) REVERT: A 331 TYR cc_start: 0.8115 (t80) cc_final: 0.7719 (t80) REVERT: A 346 SER cc_start: 0.8343 (t) cc_final: 0.7847 (p) REVERT: A 391 MET cc_start: 0.8076 (mtp) cc_final: 0.7759 (mtt) REVERT: A 471 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 491 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: A 619 LEU cc_start: 0.8196 (mp) cc_final: 0.7957 (mp) REVERT: B 267 THR cc_start: 0.8430 (m) cc_final: 0.8116 (p) REVERT: B 401 LEU cc_start: 0.7480 (tp) cc_final: 0.7213 (tt) REVERT: B 563 MET cc_start: 0.6976 (mtp) cc_final: 0.6699 (mtm) REVERT: B 587 MET cc_start: 0.6794 (tpp) cc_final: 0.6446 (tpp) REVERT: B 634 ASP cc_start: 0.7614 (m-30) cc_final: 0.7314 (m-30) REVERT: B 639 MET cc_start: 0.8510 (mmm) cc_final: 0.8170 (mmt) REVERT: B 738 ASN cc_start: 0.8042 (m-40) cc_final: 0.7709 (m-40) REVERT: B 843 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6701 (ttp-110) outliers start: 28 outliers final: 13 residues processed: 236 average time/residue: 0.2861 time to fit residues: 94.7964 Evaluate side-chains 184 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.0270 chunk 44 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 138 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 102 optimal weight: 0.0040 overall best weight: 0.4050 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 752 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.181334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139204 restraints weight = 17903.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139572 restraints weight = 16940.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140562 restraints weight = 15101.766| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13330 Z= 0.123 Angle : 0.586 11.104 18120 Z= 0.311 Chirality : 0.040 0.189 2130 Planarity : 0.004 0.037 2161 Dihedral : 14.466 145.943 2122 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.21 % Allowed : 10.18 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1550 helix: 0.10 (0.17), residues: 904 sheet: 0.20 (0.37), residues: 160 loop : 0.20 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 588 HIS 0.006 0.001 HIS A 366 PHE 0.013 0.001 PHE B 670 TYR 0.017 0.001 TYR B 303 ARG 0.004 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 639) hydrogen bonds : angle 4.37336 ( 1839) covalent geometry : bond 0.00269 (13330) covalent geometry : angle 0.58607 (18120) *********************** 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 226 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.366 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 168 VAL cc_start: 0.8286 (t) cc_final: 0.8084 (m) REVERT: A 265 SER cc_start: 0.8219 (m) cc_final: 0.7957 (t) REVERT: A 331 TYR cc_start: 0.7856 (t80) cc_final: 0.7535 (t80) REVERT: A 346 SER cc_start: 0.8320 (t) cc_final: 0.7791 (p) REVERT: A 392 ASP cc_start: 0.7717 (t0) cc_final: 0.6659 (t0) REVERT: A 718 ARG cc_start: 0.7386 (ttt180) cc_final: 0.6365 (tpt-90) REVERT: B 267 THR cc_start: 0.8341 (m) cc_final: 0.8022 (p) REVERT: B 279 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7362 (t0) REVERT: B 391 MET cc_start: 0.7221 (tpp) cc_final: 0.6749 (mmm) REVERT: B 587 MET cc_start: 0.6853 (tpp) cc_final: 0.6453 (tpp) REVERT: B 634 ASP cc_start: 0.7879 (m-30) cc_final: 0.7616 (m-30) REVERT: B 738 ASN cc_start: 0.7964 (m-40) cc_final: 0.7659 (m-40) REVERT: B 843 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6630 (ttp-110) outliers start: 30 outliers final: 15 residues processed: 218 average time/residue: 0.2760 time to fit residues: 85.8412 Evaluate side-chains 182 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 654 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 758 TYR 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 101 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 363 ASN B 85 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136218 restraints weight = 18349.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134889 restraints weight = 20595.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135097 restraints weight = 19577.716| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13330 Z= 0.165 Angle : 0.623 12.024 18120 Z= 0.322 Chirality : 0.041 0.206 2130 Planarity : 0.004 0.055 2161 Dihedral : 14.432 143.371 2122 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.58 % Allowed : 11.43 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1550 helix: 0.12 (0.17), residues: 916 sheet: -0.22 (0.40), residues: 142 loop : 0.15 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 588 HIS 0.016 0.001 HIS B 325 PHE 0.039 0.002 PHE B 87 TYR 0.024 0.002 TYR B 303 ARG 0.009 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 639) hydrogen bonds : angle 4.36420 ( 1839) covalent geometry : bond 0.00389 (13330) covalent geometry : angle 0.62277 (18120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.320 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: 0.7889 (t80) cc_final: 0.7567 (t80) REVERT: A 346 SER cc_start: 0.8304 (t) cc_final: 0.7806 (p) REVERT: A 718 ARG cc_start: 0.7466 (ttt180) cc_final: 0.5860 (tpt-90) REVERT: A 776 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 267 THR cc_start: 0.8354 (m) cc_final: 0.8066 (p) REVERT: B 395 ARG cc_start: 0.7655 (ptp-110) cc_final: 0.7454 (ptp90) REVERT: B 587 MET cc_start: 0.7025 (tpp) cc_final: 0.6656 (tpp) REVERT: B 634 ASP cc_start: 0.8070 (m-30) cc_final: 0.7720 (m-30) REVERT: B 738 ASN cc_start: 0.7959 (m-40) cc_final: 0.7630 (m-40) REVERT: B 783 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7376 (pttt) REVERT: B 843 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6776 (ttp-110) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.2706 time to fit residues: 75.0243 Evaluate side-chains 186 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 401 LEU 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 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 3 optimal weight: 0.0040 chunk 150 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** 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 = 0.4191 r_free = 0.4191 target = 0.178541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136137 restraints weight = 18248.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134535 restraints weight = 19371.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136013 restraints weight = 17036.995| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13330 Z= 0.148 Angle : 0.597 12.508 18120 Z= 0.310 Chirality : 0.040 0.150 2130 Planarity : 0.004 0.036 2161 Dihedral : 14.407 141.064 2122 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.29 % Allowed : 12.24 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1550 helix: 0.23 (0.17), residues: 918 sheet: -0.09 (0.38), residues: 160 loop : 0.15 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.005 0.001 HIS B 417 PHE 0.019 0.001 PHE B 670 TYR 0.018 0.001 TYR B 303 ARG 0.010 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 639) hydrogen bonds : angle 4.25786 ( 1839) covalent geometry : bond 0.00350 (13330) covalent geometry : angle 0.59743 (18120) *********************** 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 210 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.7922 (t80) cc_final: 0.7613 (t80) REVERT: A 346 SER cc_start: 0.8260 (t) cc_final: 0.7734 (p) REVERT: A 718 ARG cc_start: 0.7528 (ttt180) cc_final: 0.6448 (tpt-90) REVERT: B 185 ASP cc_start: 0.7769 (m-30) cc_final: 0.7467 (m-30) REVERT: B 587 MET cc_start: 0.6959 (tpp) cc_final: 0.6594 (tpp) REVERT: B 634 ASP cc_start: 0.8145 (m-30) cc_final: 0.7787 (m-30) REVERT: B 738 ASN cc_start: 0.7914 (m-40) cc_final: 0.7597 (m-40) REVERT: B 783 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7374 (pttt) REVERT: B 833 LEU cc_start: 0.8036 (mp) cc_final: 0.7588 (mp) REVERT: B 843 ARG cc_start: 0.7273 (mtp85) cc_final: 0.6820 (ttp-110) outliers start: 31 outliers final: 26 residues processed: 199 average time/residue: 0.2538 time to fit residues: 72.6137 Evaluate side-chains 192 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 401 LEU 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 655 THR 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 71 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 672 LEU 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 148 optimal weight: 8.9990 chunk 138 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4204 r_free = 0.4204 target = 0.179503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137925 restraints weight = 18199.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136574 restraints weight = 16670.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137599 restraints weight = 16510.508| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4317 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= 0.125 Angle : 0.584 13.091 18120 Z= 0.301 Chirality : 0.039 0.146 2130 Planarity : 0.003 0.036 2161 Dihedral : 14.270 139.551 2122 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.43 % Allowed : 12.83 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1550 helix: 0.41 (0.17), residues: 920 sheet: -0.04 (0.38), residues: 160 loop : 0.17 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 863 HIS 0.003 0.001 HIS B 417 PHE 0.016 0.001 PHE A 93 TYR 0.015 0.001 TYR B 303 ARG 0.006 0.000 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 639) hydrogen bonds : angle 4.16084 ( 1839) covalent geometry : bond 0.00284 (13330) covalent geometry : angle 0.58366 (18120) *********************** 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 204 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.342 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 331 TYR cc_start: 0.8067 (t80) cc_final: 0.7792 (t80) REVERT: A 346 SER cc_start: 0.8201 (t) cc_final: 0.7681 (p) REVERT: A 718 ARG cc_start: 0.7360 (ttt180) cc_final: 0.6262 (tpt-90) REVERT: B 239 TYR cc_start: 0.7850 (t80) cc_final: 0.7644 (t80) REVERT: B 316 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6201 (pmm) REVERT: B 521 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6720 (ttp80) REVERT: B 587 MET cc_start: 0.6962 (tpp) cc_final: 0.6559 (tpp) REVERT: B 634 ASP cc_start: 0.7999 (m-30) cc_final: 0.7604 (m-30) REVERT: B 738 ASN cc_start: 0.7845 (m-40) cc_final: 0.7533 (m-40) REVERT: B 806 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6677 (mtp85) REVERT: B 843 ARG cc_start: 0.7306 (mtp85) cc_final: 0.6764 (ttp-110) outliers start: 33 outliers final: 22 residues processed: 190 average time/residue: 0.2906 time to fit residues: 77.6365 Evaluate side-chains 186 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 316 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4196 r_free = 0.4196 target = 0.178675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136707 restraints weight = 18084.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135904 restraints weight = 16946.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137198 restraints weight = 16581.313| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4456 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 12.201 18120 Z= 0.305 Chirality : 0.040 0.151 2130 Planarity : 0.004 0.037 2161 Dihedral : 14.188 137.792 2122 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.06 % Allowed : 14.23 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1550 helix: 0.53 (0.17), residues: 908 sheet: 0.09 (0.38), residues: 154 loop : 0.09 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 PHE 0.017 0.001 PHE A 670 TYR 0.013 0.001 TYR B 303 ARG 0.014 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 639) hydrogen bonds : angle 4.17402 ( 1839) covalent geometry : bond 0.00310 (13330) covalent geometry : angle 0.59422 (18120) *********************** 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 195 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.363 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 346 SER cc_start: 0.8116 (t) cc_final: 0.7682 (p) REVERT: A 718 ARG cc_start: 0.7455 (ttt180) cc_final: 0.6334 (tpt-90) REVERT: B 316 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6213 (pmm) REVERT: B 537 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6574 (mt-10) REVERT: B 587 MET cc_start: 0.6955 (tpp) cc_final: 0.6541 (tpp) REVERT: B 634 ASP cc_start: 0.7915 (m-30) cc_final: 0.7497 (m-30) REVERT: B 738 ASN cc_start: 0.7862 (m-40) cc_final: 0.7550 (m-40) REVERT: B 783 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7304 (pttt) REVERT: B 806 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6609 (mtp85) REVERT: B 843 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6797 (ttp-110) outliers start: 28 outliers final: 22 residues processed: 185 average time/residue: 0.2895 time to fit residues: 75.5059 Evaluate side-chains 177 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 71 LEU 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 316 MET 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 69 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.178848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136024 restraints weight = 18271.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134325 restraints weight = 18101.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135125 restraints weight = 16274.908| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13330 Z= 0.135 Angle : 0.600 14.442 18120 Z= 0.306 Chirality : 0.040 0.183 2130 Planarity : 0.004 0.040 2161 Dihedral : 14.193 139.240 2122 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.29 % Allowed : 14.01 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1550 helix: 0.54 (0.17), residues: 908 sheet: 0.07 (0.38), residues: 154 loop : 0.12 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 95 HIS 0.006 0.001 HIS A 417 PHE 0.017 0.001 PHE A 432 TYR 0.048 0.001 TYR A 331 ARG 0.014 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 639) hydrogen bonds : angle 4.17691 ( 1839) covalent geometry : bond 0.00314 (13330) covalent geometry : angle 0.60018 (18120) *********************** 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 196 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.319 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: 0.7399 (p) cc_final: 0.7027 (m) REVERT: A 346 SER cc_start: 0.7954 (t) cc_final: 0.7527 (p) REVERT: A 473 THR cc_start: 0.8426 (m) cc_final: 0.8194 (t) REVERT: A 718 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6331 (tpt-90) REVERT: B 316 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6201 (pmm) REVERT: B 537 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6454 (mt-10) REVERT: B 587 MET cc_start: 0.7017 (tpp) cc_final: 0.6616 (tpp) REVERT: B 634 ASP cc_start: 0.8039 (m-30) cc_final: 0.7639 (m-30) REVERT: B 738 ASN cc_start: 0.7877 (m-40) cc_final: 0.7559 (m-40) REVERT: B 783 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7351 (pttt) REVERT: B 843 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6791 (ttp-110) outliers start: 31 outliers final: 24 residues processed: 187 average time/residue: 0.2821 time to fit residues: 75.3924 Evaluate side-chains 183 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 758 TYR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 71 LEU 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 316 MET 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 71 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 63 optimal weight: 0.0470 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN A 451 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138271 restraints weight = 18284.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136336 restraints weight = 19500.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138088 restraints weight = 17943.381| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4685 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= 0.131 Angle : 0.607 13.972 18120 Z= 0.307 Chirality : 0.040 0.180 2130 Planarity : 0.004 0.040 2161 Dihedral : 14.182 139.796 2122 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 14.09 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1550 helix: 0.58 (0.17), residues: 908 sheet: 0.14 (0.38), residues: 154 loop : 0.09 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 95 HIS 0.004 0.001 HIS B 417 PHE 0.016 0.001 PHE A 670 TYR 0.012 0.001 TYR B 303 ARG 0.014 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 639) hydrogen bonds : angle 4.16379 ( 1839) covalent geometry : bond 0.00307 (13330) covalent geometry : angle 0.60727 (18120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.562 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: 0.7358 (p) cc_final: 0.7032 (m) REVERT: A 331 TYR cc_start: 0.7971 (t80) cc_final: 0.7717 (t80) REVERT: A 346 SER cc_start: 0.8085 (t) cc_final: 0.7631 (p) REVERT: A 452 LEU cc_start: 0.8171 (mm) cc_final: 0.7941 (mt) REVERT: A 718 ARG cc_start: 0.7541 (ttt180) cc_final: 0.6347 (tpt-90) REVERT: B 316 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.6120 (pmm) REVERT: B 537 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6393 (mt-10) REVERT: B 587 MET cc_start: 0.6852 (tpp) cc_final: 0.6478 (tpp) REVERT: B 634 ASP cc_start: 0.8085 (m-30) cc_final: 0.7691 (m-30) REVERT: B 738 ASN cc_start: 0.7848 (m-40) cc_final: 0.7549 (m-40) REVERT: B 783 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7351 (pttt) REVERT: B 843 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6750 (ttp-110) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.2825 time to fit residues: 76.0312 Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 350 CYS Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 401 LEU 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 A residue 767 ASN Chi-restraints excluded: chain B residue 71 LEU 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 316 MET 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 146 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 138 optimal weight: 0.0070 chunk 134 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.180508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138486 restraints weight = 18138.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135179 restraints weight = 19480.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135749 restraints weight = 18434.873| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13330 Z= 0.118 Angle : 0.610 13.891 18120 Z= 0.309 Chirality : 0.040 0.273 2130 Planarity : 0.004 0.040 2161 Dihedral : 14.133 139.885 2122 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.92 % Allowed : 14.45 % Favored : 83.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1550 helix: 0.62 (0.17), residues: 906 sheet: 0.21 (0.38), residues: 154 loop : 0.12 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 95 HIS 0.004 0.001 HIS A 338 PHE 0.023 0.001 PHE A 432 TYR 0.011 0.001 TYR B 303 ARG 0.016 0.000 ARG B 884 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 639) hydrogen bonds : angle 4.14198 ( 1839) covalent geometry : bond 0.00266 (13330) covalent geometry : angle 0.61044 (18120) ********************** 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 201 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.525 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 295 SER cc_start: 0.7368 (p) cc_final: 0.7013 (m) REVERT: A 331 TYR cc_start: 0.8257 (t80) cc_final: 0.7841 (t80) REVERT: A 346 SER cc_start: 0.7945 (t) cc_final: 0.7492 (p) REVERT: A 392 ASP cc_start: 0.8024 (t0) cc_final: 0.7424 (m-30) REVERT: A 395 ARG cc_start: 0.7887 (ptp90) cc_final: 0.7331 (mtm-85) REVERT: A 718 ARG cc_start: 0.7530 (ttt180) cc_final: 0.6327 (tpt-90) REVERT: B 316 MET cc_start: 0.6708 (pmm) cc_final: 0.6249 (pmm) REVERT: B 537 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6399 (mt-10) REVERT: B 587 MET cc_start: 0.6971 (tpp) cc_final: 0.6560 (tpp) REVERT: B 634 ASP cc_start: 0.7867 (m-30) cc_final: 0.7437 (m-30) REVERT: B 738 ASN cc_start: 0.7776 (m-40) cc_final: 0.7442 (m-40) REVERT: B 783 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7330 (pttt) REVERT: B 843 ARG cc_start: 0.7263 (mtp85) cc_final: 0.6688 (ttp-110) outliers start: 26 outliers final: 22 residues processed: 194 average time/residue: 0.3017 time to fit residues: 84.7861 Evaluate side-chains 185 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 417 HIS 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 A residue 767 ASN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 806 ARG 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 143 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 30 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4188 r_free = 0.4188 target = 0.178188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138251 restraints weight = 18124.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136120 restraints weight = 18028.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137390 restraints weight = 20133.026| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4818 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= 0.162 Angle : 0.649 13.538 18120 Z= 0.329 Chirality : 0.042 0.260 2130 Planarity : 0.004 0.042 2161 Dihedral : 14.270 140.174 2122 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.70 % Allowed : 15.27 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1550 helix: 0.54 (0.17), residues: 902 sheet: -0.01 (0.41), residues: 134 loop : 0.05 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 95 HIS 0.006 0.001 HIS A 417 PHE 0.027 0.002 PHE A 432 TYR 0.015 0.001 TYR A 155 ARG 0.014 0.001 ARG B 884 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 639) hydrogen bonds : angle 4.27068 ( 1839) covalent geometry : bond 0.00386 (13330) covalent geometry : angle 0.64892 (18120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.72 seconds wall clock time: 76 minutes 10.86 seconds (4570.86 seconds total)