Starting phenix.real_space_refine on Wed Mar 12 11:25:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095.map" model { file = "/net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bgi_7095/03_2025/6bgi_7095_neut.cif" } resolution = 3.8 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= 0.000 sd= 1.000 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 Ca 4 9.91 5 S 50 5.16 5 C 5120 2.51 5 N 1266 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3885 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 20, 'TRANS': 489} Chain breaks: 3 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3885 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 20, 'TRANS': 489} Chain breaks: 3 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.14, per 1000 atoms: 0.66 Number of scatterers: 7774 At special positions: 0 Unit cell: (131.58, 83.64, 104.04, 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) Ca 4 19.99 S 50 16.00 O 1334 8.00 N 1266 7.00 C 5120 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.140A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 326 through 362 removed outlier: 3.707A pdb=" N PHE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.514A pdb=" N VAL A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.851A pdb=" N ILE A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.796A pdb=" N ASP A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.979A pdb=" N THR A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 440 removed outlier: 4.346A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.519A pdb=" N ALA A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.609A pdb=" N TYR A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 563 removed outlier: 3.812A pdb=" N ALA A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 562 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 597 removed outlier: 3.504A pdb=" N ARG A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.275A pdb=" N PHE A 613 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 646 removed outlier: 4.117A pdb=" N CYS A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 removed outlier: 3.577A pdb=" N ILE A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Proline residue: A 654 - end of helix Processing helix chain 'A' and resid 657 through 667 Processing helix chain 'A' and resid 684 through 688 removed outlier: 3.672A pdb=" N PHE A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 711 removed outlier: 3.593A pdb=" N GLU A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 741 removed outlier: 3.523A pdb=" N PHE A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 removed outlier: 4.407A pdb=" N ILE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 781 through 789 removed outlier: 5.956A pdb=" N TYR A 787 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.869A pdb=" N GLY A 799 " --> pdb=" O THR A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 808 removed outlier: 4.611A pdb=" N LEU A 805 " --> pdb=" O VAL A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 removed outlier: 3.683A pdb=" N THR A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 813 through 818' Processing helix chain 'A' and resid 820 through 825 removed outlier: 4.000A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 882 removed outlier: 3.834A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 870 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 878 " --> pdb=" O MET A 874 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 removed outlier: 4.140A pdb=" N ARG B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 326 through 362 removed outlier: 3.707A pdb=" N PHE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 342 " --> pdb=" O TYR B 338 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.513A pdb=" N VAL B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.850A pdb=" N ILE B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.796A pdb=" N ASP B 383 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.978A pdb=" N THR B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 440 removed outlier: 4.346A pdb=" N VAL B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.520A pdb=" N ALA B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.608A pdb=" N TYR B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 514 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 563 removed outlier: 3.812A pdb=" N ALA B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 544 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 545 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 551 " --> pdb=" O ILE B 547 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 562 " --> pdb=" O ARG B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 removed outlier: 3.503A pdb=" N ARG B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 590 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Proline residue: B 591 - end of helix Processing helix chain 'B' and resid 608 through 613 removed outlier: 4.275A pdb=" N PHE B 613 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 646 removed outlier: 4.117A pdb=" N CYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 657 removed outlier: 3.577A pdb=" N ILE B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) Proline residue: B 654 - end of helix Processing helix chain 'B' and resid 657 through 667 Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.672A pdb=" N PHE B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 711 removed outlier: 3.593A pdb=" N GLU B 698 " --> pdb=" O GLY B 694 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 741 removed outlier: 3.523A pdb=" N PHE B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 723 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 767 removed outlier: 4.407A pdb=" N ILE B 759 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 777 Processing helix chain 'B' and resid 781 through 789 removed outlier: 5.956A pdb=" N TYR B 787 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.869A pdb=" N GLY B 799 " --> pdb=" O THR B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 808 removed outlier: 4.610A pdb=" N LEU B 805 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.683A pdb=" N THR B 817 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 818' Processing helix chain 'B' and resid 820 through 825 removed outlier: 4.000A pdb=" N ASP B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 882 removed outlier: 3.834A pdb=" N VAL B 856 " --> pdb=" O ASP B 852 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 864 " --> pdb=" O ARG B 860 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 870 " --> pdb=" O VAL B 866 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 2.43 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: 2375 1.34 - 1.46: 1787 1.46 - 1.58: 3722 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 7964 Sorted by residual: bond pdb=" CG1 ILE A 703 " pdb=" CD1 ILE A 703 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" CE2 TRP A 419 " pdb=" CZ2 TRP A 419 " ideal model delta sigma weight residual 1.394 1.362 0.032 2.10e-02 2.27e+03 2.35e+00 bond pdb=" CA LEU B 627 " pdb=" C LEU B 627 " ideal model delta sigma weight residual 1.532 1.518 0.015 9.60e-03 1.09e+04 2.35e+00 bond pdb=" CG1 ILE B 703 " pdb=" CD1 ILE B 703 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.34e+00 bond pdb=" CE2 TRP B 419 " pdb=" CZ2 TRP B 419 " ideal model delta sigma weight residual 1.394 1.362 0.032 2.10e-02 2.27e+03 2.25e+00 ... (remaining 7959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 10300 2.03 - 4.06: 456 4.06 - 6.09: 56 6.09 - 8.11: 20 8.11 - 10.14: 4 Bond angle restraints: 10836 Sorted by residual: angle pdb=" N ALA A 306 " pdb=" CA ALA A 306 " pdb=" C ALA A 306 " ideal model delta sigma weight residual 111.03 105.40 5.63 1.11e+00 8.12e-01 2.58e+01 angle pdb=" N ALA B 306 " pdb=" CA ALA B 306 " pdb=" C ALA B 306 " ideal model delta sigma weight residual 111.03 105.42 5.61 1.11e+00 8.12e-01 2.56e+01 angle pdb=" N LEU B 403 " pdb=" CA LEU B 403 " pdb=" C LEU B 403 " ideal model delta sigma weight residual 114.75 108.87 5.88 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N LEU A 403 " pdb=" CA LEU A 403 " pdb=" C LEU A 403 " ideal model delta sigma weight residual 114.75 108.90 5.85 1.26e+00 6.30e-01 2.16e+01 angle pdb=" N VAL B 739 " pdb=" CA VAL B 739 " pdb=" C VAL B 739 " ideal model delta sigma weight residual 111.45 107.27 4.18 9.30e-01 1.16e+00 2.02e+01 ... (remaining 10831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.45: 3854 8.45 - 16.90: 645 16.90 - 25.35: 107 25.35 - 33.80: 36 33.80 - 42.25: 14 Dihedral angle restraints: 4656 sinusoidal: 1658 harmonic: 2998 Sorted by residual: dihedral pdb=" CA LYS A 751 " pdb=" C LYS A 751 " pdb=" N ASP A 752 " pdb=" CA ASP A 752 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LYS B 751 " pdb=" C LYS B 751 " pdb=" N ASP B 752 " pdb=" CA ASP B 752 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE B 404 " pdb=" C PHE B 404 " pdb=" N ASP B 405 " pdb=" CA ASP B 405 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 518 0.029 - 0.057: 416 0.057 - 0.085: 219 0.085 - 0.113: 72 0.113 - 0.142: 25 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CA ASP A 780 " pdb=" N ASP A 780 " pdb=" C ASP A 780 " pdb=" CB ASP A 780 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ASP B 780 " pdb=" N ASP B 780 " pdb=" C ASP B 780 " pdb=" CB ASP B 780 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL B 310 " pdb=" N VAL B 310 " pdb=" C VAL B 310 " pdb=" CB VAL B 310 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1247 not shown) Planarity restraints: 1354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 708 " 0.017 2.00e-02 2.50e+03 2.06e-02 7.40e+00 pdb=" CG PHE A 708 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 708 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 708 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 708 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 708 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 708 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 708 " 0.017 2.00e-02 2.50e+03 2.04e-02 7.27e+00 pdb=" CG PHE B 708 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 708 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 708 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 708 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 708 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 708 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 407 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.028 5.00e-02 4.00e+02 ... (remaining 1351 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 108 2.58 - 3.16: 8035 3.16 - 3.74: 11318 3.74 - 4.32: 16991 4.32 - 4.90: 24947 Nonbonded interactions: 61399 Sorted by model distance: nonbonded pdb=" OE1 GLU A 650 " pdb="CA CA A1001 " model vdw 2.002 2.510 nonbonded pdb=" O VAL A 586 " pdb=" OG1 THR A 590 " model vdw 2.046 3.040 nonbonded pdb=" O VAL B 586 " pdb=" OG1 THR B 590 " model vdw 2.047 3.040 nonbonded pdb=" O LEU A 643 " pdb="CA CA A1002 " model vdw 2.119 2.510 nonbonded pdb=" O ASN B 802 " pdb=" OG SER B 806 " model vdw 2.133 3.040 ... (remaining 61394 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: 0.04 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: 0.800 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 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 : 0.008 0.060 7964 Z= 0.490 Angle : 0.999 10.144 10836 Z= 0.578 Chirality : 0.049 0.142 1250 Planarity : 0.005 0.049 1354 Dihedral : 8.911 42.252 2712 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 48.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.14 % Favored : 83.86 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -5.29 (0.22), residues: 1004 helix: -3.29 (0.15), residues: 610 sheet: None (None), residues: 0 loop : -3.70 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 854 HIS 0.008 0.002 HIS A 803 PHE 0.046 0.004 PHE A 708 TYR 0.019 0.002 TYR B 589 ARG 0.008 0.001 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TRP cc_start: 0.7904 (t60) cc_final: 0.7059 (t60) REVERT: A 391 MET cc_start: 0.6009 (mtp) cc_final: 0.5742 (mtp) REVERT: A 427 TRP cc_start: 0.7611 (t-100) cc_final: 0.7386 (t-100) REVERT: A 543 LEU cc_start: 0.7956 (mp) cc_final: 0.7626 (mp) REVERT: A 639 LEU cc_start: 0.6946 (mt) cc_final: 0.6343 (mt) REVERT: A 751 LYS cc_start: 0.5630 (mttt) cc_final: 0.5238 (mmtp) REVERT: B 296 ASN cc_start: 0.7113 (m-40) cc_final: 0.6908 (m-40) REVERT: B 300 LEU cc_start: 0.8813 (mt) cc_final: 0.8507 (mt) REVERT: B 334 TRP cc_start: 0.8054 (t60) cc_final: 0.7191 (t60) REVERT: B 643 LEU cc_start: 0.7393 (mt) cc_final: 0.7164 (mt) REVERT: B 751 LYS cc_start: 0.5448 (mttt) cc_final: 0.4765 (ttmt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2424 time to fit residues: 86.1233 Evaluate side-chains 178 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 92 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 727 ASN A 803 HIS ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 HIS ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.199475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.163067 restraints weight = 16210.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.167085 restraints weight = 9570.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.169832 restraints weight = 6909.389| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 7964 Z= 0.261 Angle : 0.816 10.072 10836 Z= 0.424 Chirality : 0.046 0.222 1250 Planarity : 0.005 0.041 1354 Dihedral : 5.654 25.254 1092 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 2.09 % Allowed : 12.17 % Favored : 85.73 % 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: -3.71 (0.24), residues: 1004 helix: -1.35 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -4.52 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 427 HIS 0.005 0.001 HIS B 402 PHE 0.024 0.002 PHE A 853 TYR 0.021 0.002 TYR A 757 ARG 0.005 0.001 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 CYS cc_start: 0.7649 (m) cc_final: 0.7242 (m) REVERT: A 578 PHE cc_start: 0.7910 (t80) cc_final: 0.7646 (t80) REVERT: A 628 MET cc_start: 0.7729 (tpp) cc_final: 0.7354 (tpp) REVERT: B 319 LEU cc_start: 0.9059 (tp) cc_final: 0.8754 (pt) REVERT: B 378 MET cc_start: 0.2001 (mtp) cc_final: 0.1402 (mtm) REVERT: B 695 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7962 (mm) REVERT: B 751 LYS cc_start: 0.5177 (mttt) cc_final: 0.4809 (ttmt) outliers start: 16 outliers final: 4 residues processed: 228 average time/residue: 0.1680 time to fit residues: 53.4038 Evaluate side-chains 181 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 84 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 794 ASN A 798 HIS ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.198508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.162120 restraints weight = 16489.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.165919 restraints weight = 10026.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.168248 restraints weight = 7488.403| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7964 Z= 0.242 Angle : 0.730 9.086 10836 Z= 0.375 Chirality : 0.044 0.203 1250 Planarity : 0.004 0.033 1354 Dihedral : 5.278 19.913 1092 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 3.27 % Allowed : 14.79 % Favored : 81.94 % 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: -2.84 (0.25), residues: 1004 helix: -0.61 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -4.39 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 427 HIS 0.002 0.001 HIS B 803 PHE 0.025 0.002 PHE A 581 TYR 0.020 0.001 TYR A 594 ARG 0.005 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TRP cc_start: 0.7821 (t-100) cc_final: 0.7421 (t-100) REVERT: A 543 LEU cc_start: 0.8486 (mp) cc_final: 0.8241 (mp) REVERT: A 628 MET cc_start: 0.7305 (tpp) cc_final: 0.6797 (tpp) REVERT: A 638 MET cc_start: 0.5351 (mmt) cc_final: 0.5127 (mmt) REVERT: A 742 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6542 (mm) REVERT: A 760 LEU cc_start: 0.9024 (tp) cc_final: 0.8677 (tp) REVERT: A 775 ILE cc_start: 0.8312 (tt) cc_final: 0.7985 (mt) REVERT: B 319 LEU cc_start: 0.9036 (tp) cc_final: 0.8652 (pt) REVERT: B 367 MET cc_start: 0.2614 (mtt) cc_final: 0.2368 (mtm) REVERT: B 574 GLU cc_start: 0.8375 (mp0) cc_final: 0.7973 (mp0) REVERT: B 751 LYS cc_start: 0.4947 (mttt) cc_final: 0.4559 (ttmt) outliers start: 25 outliers final: 11 residues processed: 213 average time/residue: 0.1626 time to fit residues: 48.7920 Evaluate side-chains 179 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.201573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.165992 restraints weight = 16406.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.169933 restraints weight = 9962.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.172633 restraints weight = 7312.115| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7964 Z= 0.195 Angle : 0.691 13.697 10836 Z= 0.351 Chirality : 0.044 0.323 1250 Planarity : 0.004 0.032 1354 Dihedral : 4.910 18.245 1092 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.14 % Allowed : 17.28 % Favored : 79.58 % 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: -2.60 (0.25), residues: 1004 helix: -0.32 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -4.72 (0.24), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 427 HIS 0.003 0.001 HIS A 803 PHE 0.018 0.001 PHE A 572 TYR 0.018 0.001 TYR A 355 ARG 0.005 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8246 (ttmt) cc_final: 0.8026 (tptp) REVERT: A 341 MET cc_start: 0.8609 (tpp) cc_final: 0.8215 (tpp) REVERT: A 399 ARG cc_start: 0.6607 (ttt-90) cc_final: 0.5565 (ptt-90) REVERT: A 427 TRP cc_start: 0.7709 (t-100) cc_final: 0.7297 (t-100) REVERT: A 496 MET cc_start: 0.6754 (pmm) cc_final: 0.6353 (pmm) REVERT: A 628 MET cc_start: 0.6875 (tpp) cc_final: 0.6594 (tpp) REVERT: A 742 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6711 (mm) REVERT: A 760 LEU cc_start: 0.8961 (tp) cc_final: 0.8703 (tp) REVERT: A 782 ILE cc_start: 0.4843 (mt) cc_final: 0.4406 (mm) REVERT: A 797 MET cc_start: 0.1891 (ptm) cc_final: 0.1662 (ptm) REVERT: B 574 GLU cc_start: 0.8356 (mp0) cc_final: 0.8054 (mp0) REVERT: B 628 MET cc_start: 0.7584 (tpp) cc_final: 0.7192 (tpp) outliers start: 24 outliers final: 14 residues processed: 206 average time/residue: 0.1933 time to fit residues: 55.0017 Evaluate side-chains 182 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.198049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.162184 restraints weight = 16011.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.166016 restraints weight = 9695.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.168583 restraints weight = 7160.733| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7964 Z= 0.233 Angle : 0.691 10.985 10836 Z= 0.355 Chirality : 0.043 0.180 1250 Planarity : 0.004 0.033 1354 Dihedral : 4.888 18.948 1092 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 4.45 % Allowed : 18.59 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.25), residues: 1004 helix: -0.06 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -4.60 (0.25), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 427 HIS 0.002 0.001 HIS B 426 PHE 0.015 0.002 PHE A 712 TYR 0.012 0.001 TYR A 331 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7993 (tptp) REVERT: A 364 ILE cc_start: 0.5665 (mm) cc_final: 0.5442 (tp) REVERT: A 399 ARG cc_start: 0.6619 (ttt-90) cc_final: 0.5529 (ptt-90) REVERT: A 427 TRP cc_start: 0.7874 (t-100) cc_final: 0.7503 (t-100) REVERT: A 628 MET cc_start: 0.6927 (tpp) cc_final: 0.6524 (tpp) REVERT: A 634 LEU cc_start: 0.7740 (mp) cc_final: 0.7494 (mt) REVERT: A 742 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6929 (mm) REVERT: A 760 LEU cc_start: 0.9012 (tp) cc_final: 0.8738 (tp) REVERT: A 797 MET cc_start: 0.1966 (ptm) cc_final: 0.1759 (ptm) REVERT: B 574 GLU cc_start: 0.8343 (mp0) cc_final: 0.8006 (mp0) REVERT: B 628 MET cc_start: 0.7579 (tpp) cc_final: 0.7291 (tpp) REVERT: B 784 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6702 (tpm170) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 0.1919 time to fit residues: 54.1718 Evaluate side-chains 187 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 60 optimal weight: 0.0060 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.199867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.163834 restraints weight = 16260.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.167611 restraints weight = 10039.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.170049 restraints weight = 7472.968| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7964 Z= 0.222 Angle : 0.695 10.761 10836 Z= 0.353 Chirality : 0.043 0.168 1250 Planarity : 0.004 0.031 1354 Dihedral : 4.820 19.789 1092 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 4.45 % Allowed : 18.98 % Favored : 76.57 % 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: -2.19 (0.25), residues: 1004 helix: -0.01 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -4.56 (0.26), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 427 HIS 0.002 0.001 HIS B 798 PHE 0.032 0.002 PHE B 581 TYR 0.010 0.001 TYR A 331 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7859 (tptp) REVERT: A 399 ARG cc_start: 0.6418 (ttt-90) cc_final: 0.5338 (ptt-90) REVERT: A 427 TRP cc_start: 0.7847 (t-100) cc_final: 0.7431 (t-100) REVERT: A 431 GLN cc_start: 0.7802 (tt0) cc_final: 0.7571 (tm-30) REVERT: A 496 MET cc_start: 0.7199 (pmm) cc_final: 0.6850 (pmm) REVERT: A 628 MET cc_start: 0.6800 (tpp) cc_final: 0.6494 (tpp) REVERT: A 760 LEU cc_start: 0.8964 (tp) cc_final: 0.8754 (tp) REVERT: A 782 ILE cc_start: 0.4699 (mt) cc_final: 0.3974 (mm) REVERT: A 797 MET cc_start: 0.1873 (ptm) cc_final: 0.1500 (ptp) REVERT: B 574 GLU cc_start: 0.8387 (mp0) cc_final: 0.8021 (mp0) REVERT: B 628 MET cc_start: 0.7549 (tpp) cc_final: 0.7210 (tpp) REVERT: B 784 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6657 (tpm170) outliers start: 34 outliers final: 19 residues processed: 190 average time/residue: 0.2135 time to fit residues: 56.3609 Evaluate side-chains 178 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.201385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.165856 restraints weight = 16262.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.169791 restraints weight = 9960.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.172373 restraints weight = 7341.937| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7964 Z= 0.188 Angle : 0.686 10.588 10836 Z= 0.343 Chirality : 0.042 0.180 1250 Planarity : 0.003 0.028 1354 Dihedral : 4.698 19.224 1092 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.01 % Allowed : 19.76 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.26), residues: 1004 helix: 0.11 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -4.50 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 427 HIS 0.003 0.001 HIS B 798 PHE 0.020 0.001 PHE A 324 TYR 0.011 0.001 TYR A 757 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.7544 (m-80) cc_final: 0.7180 (m-10) REVERT: A 327 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7868 (tptp) REVERT: A 399 ARG cc_start: 0.6425 (ttt-90) cc_final: 0.5345 (ptt-90) REVERT: A 427 TRP cc_start: 0.7778 (t-100) cc_final: 0.7428 (t-100) REVERT: A 496 MET cc_start: 0.7151 (pmm) cc_final: 0.6870 (pmm) REVERT: A 628 MET cc_start: 0.6903 (tpp) cc_final: 0.6537 (tpp) REVERT: A 797 MET cc_start: 0.1832 (ptm) cc_final: 0.1444 (ptp) REVERT: B 496 MET cc_start: 0.7325 (pmm) cc_final: 0.6253 (mpp) REVERT: B 574 GLU cc_start: 0.8270 (mp0) cc_final: 0.7998 (mp0) REVERT: B 628 MET cc_start: 0.7512 (tpp) cc_final: 0.7209 (tpp) REVERT: B 751 LYS cc_start: 0.4722 (ttmt) cc_final: 0.4432 (ttpt) REVERT: B 784 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6412 (tpm170) outliers start: 23 outliers final: 18 residues processed: 189 average time/residue: 0.2239 time to fit residues: 59.7284 Evaluate side-chains 185 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.0060 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 809 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.202515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.166474 restraints weight = 16348.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.170445 restraints weight = 10002.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.173031 restraints weight = 7317.449| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7964 Z= 0.182 Angle : 0.690 13.373 10836 Z= 0.346 Chirality : 0.042 0.195 1250 Planarity : 0.003 0.029 1354 Dihedral : 4.599 18.966 1092 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.66 % Allowed : 20.16 % Favored : 76.18 % 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: -1.78 (0.26), residues: 1004 helix: 0.32 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.51 (0.26), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 427 HIS 0.003 0.001 HIS A 798 PHE 0.031 0.001 PHE A 722 TYR 0.015 0.001 TYR A 355 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.7560 (m-80) cc_final: 0.7149 (m-10) REVERT: A 327 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7801 (tptp) REVERT: A 399 ARG cc_start: 0.6468 (ttt-90) cc_final: 0.5359 (ptt-90) REVERT: A 416 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7072 (mmm) REVERT: A 427 TRP cc_start: 0.7902 (t-100) cc_final: 0.7527 (t-100) REVERT: A 628 MET cc_start: 0.6770 (tpp) cc_final: 0.6412 (tpp) REVERT: A 797 MET cc_start: 0.1689 (ptm) cc_final: 0.1342 (ptp) REVERT: B 428 LYS cc_start: 0.7995 (tptp) cc_final: 0.7775 (ttpt) REVERT: B 574 GLU cc_start: 0.8363 (mp0) cc_final: 0.8078 (mp0) REVERT: B 628 MET cc_start: 0.7467 (tpp) cc_final: 0.7198 (tpp) REVERT: B 751 LYS cc_start: 0.4679 (ttmt) cc_final: 0.4446 (ttpt) REVERT: B 784 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6372 (tpm170) outliers start: 28 outliers final: 20 residues processed: 191 average time/residue: 0.1689 time to fit residues: 45.0425 Evaluate side-chains 187 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.202801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.166936 restraints weight = 16502.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.170818 restraints weight = 10052.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.173438 restraints weight = 7419.033| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7964 Z= 0.197 Angle : 0.720 12.679 10836 Z= 0.359 Chirality : 0.042 0.194 1250 Planarity : 0.003 0.031 1354 Dihedral : 4.546 18.735 1092 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.66 % Allowed : 20.29 % Favored : 76.05 % 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: -1.68 (0.26), residues: 1004 helix: 0.37 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.39 (0.27), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 427 HIS 0.003 0.001 HIS B 798 PHE 0.018 0.001 PHE B 581 TYR 0.011 0.001 TYR A 699 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.7577 (m-80) cc_final: 0.7162 (m-10) REVERT: A 334 TRP cc_start: 0.7781 (t60) cc_final: 0.7279 (t60) REVERT: A 399 ARG cc_start: 0.6444 (ttt-90) cc_final: 0.5375 (ptt-90) REVERT: A 427 TRP cc_start: 0.7937 (t-100) cc_final: 0.7573 (t-100) REVERT: A 628 MET cc_start: 0.6736 (tpp) cc_final: 0.6415 (tpp) REVERT: A 797 MET cc_start: 0.1676 (ptm) cc_final: 0.1339 (ptp) REVERT: B 497 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7979 (mt) REVERT: B 574 GLU cc_start: 0.8376 (mp0) cc_final: 0.8088 (mp0) REVERT: B 628 MET cc_start: 0.7451 (tpp) cc_final: 0.7210 (tpp) REVERT: B 749 ARG cc_start: 0.4749 (mmt180) cc_final: 0.4087 (mmt180) REVERT: B 751 LYS cc_start: 0.4446 (ttmt) cc_final: 0.4163 (ttpt) REVERT: B 784 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6415 (tpm170) outliers start: 28 outliers final: 23 residues processed: 194 average time/residue: 0.2422 time to fit residues: 64.9422 Evaluate side-chains 193 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 305 TRP Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.202980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.167502 restraints weight = 16478.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.171244 restraints weight = 10251.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.173792 restraints weight = 7599.031| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7964 Z= 0.198 Angle : 0.721 12.466 10836 Z= 0.361 Chirality : 0.043 0.196 1250 Planarity : 0.003 0.031 1354 Dihedral : 4.513 18.835 1092 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.01 % Allowed : 21.60 % Favored : 75.39 % 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: -1.54 (0.26), residues: 1004 helix: 0.46 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.30 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 427 HIS 0.002 0.001 HIS B 798 PHE 0.031 0.002 PHE A 722 TYR 0.013 0.001 TYR A 699 ARG 0.003 0.000 ARG A 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.7512 (m-80) cc_final: 0.7035 (m-10) REVERT: A 334 TRP cc_start: 0.7821 (t60) cc_final: 0.7291 (t60) REVERT: A 399 ARG cc_start: 0.6487 (ttt-90) cc_final: 0.5379 (ptt-90) REVERT: A 427 TRP cc_start: 0.7974 (t-100) cc_final: 0.7550 (t-100) REVERT: A 628 MET cc_start: 0.6748 (tpp) cc_final: 0.6399 (tpp) REVERT: A 797 MET cc_start: 0.1498 (ptm) cc_final: 0.1178 (ptp) REVERT: B 497 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 574 GLU cc_start: 0.8368 (mp0) cc_final: 0.8088 (mp0) REVERT: B 628 MET cc_start: 0.7348 (tpp) cc_final: 0.7032 (tpp) REVERT: B 749 ARG cc_start: 0.4975 (mmt180) cc_final: 0.4310 (mmt180) REVERT: B 751 LYS cc_start: 0.4516 (ttmt) cc_final: 0.4311 (ttpt) REVERT: B 784 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6197 (tpm170) outliers start: 23 outliers final: 18 residues processed: 193 average time/residue: 0.2166 time to fit residues: 58.6455 Evaluate side-chains 184 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.199252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.163613 restraints weight = 16174.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.167310 restraints weight = 9903.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.169220 restraints weight = 7331.707| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7964 Z= 0.223 Angle : 0.730 12.287 10836 Z= 0.367 Chirality : 0.044 0.201 1250 Planarity : 0.003 0.030 1354 Dihedral : 4.589 19.880 1092 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.27 % Allowed : 20.55 % Favored : 76.18 % 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: -1.50 (0.26), residues: 1004 helix: 0.51 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -4.30 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 427 HIS 0.011 0.002 HIS A 426 PHE 0.029 0.002 PHE A 581 TYR 0.010 0.001 TYR B 338 ARG 0.002 0.000 ARG A 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.50 seconds wall clock time: 52 minutes 53.84 seconds (3173.84 seconds total)