Starting phenix.real_space_refine on Fri Aug 22 20:41:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bgi_7095/08_2025/6bgi_7095_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bgi_7095/08_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_7095/08_2025/6bgi_7095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bgi_7095/08_2025/6bgi_7095.map" model { file = "/net/cci-nas-00/data/ceres_data/6bgi_7095/08_2025/6bgi_7095_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bgi_7095/08_2025/6bgi_7095_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ASN:plan1': 4, 'TYR:plan': 4, 'TRP:plan': 2, 'PHE:plan': 4, 'ARG:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1} 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: {'GLU:plan': 8, 'ASN:plan1': 4, 'TYR:plan': 4, 'TRP:plan': 2, 'PHE:plan': 4, 'ARG:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1} 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: 1.75, per 1000 atoms: 0.23 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: 0.61 Conformation dependent library (CDL) restraints added in 448.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 1.16 Time building geometry restraints manager: 0.86 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: 0.02 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: 1.030 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- 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= 0.360 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 : 48.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG A 860 TYR 0.019 0.002 TYR B 589 PHE 0.046 0.004 PHE A 708 TRP 0.031 0.004 TRP B 854 HIS 0.008 0.002 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00756 ( 7964) covalent geometry : angle 0.99896 (10836) hydrogen bonds : bond 0.35387 ( 417) hydrogen bonds : angle 12.17989 ( 1233) *********************** 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 : 0.287 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: 0.7061 (t60) REVERT: A 391 MET cc_start: 0.6009 (mtp) cc_final: 0.5750 (mtp) REVERT: A 427 TRP cc_start: 0.7611 (t-100) cc_final: 0.7384 (t-100) REVERT: A 543 LEU cc_start: 0.7956 (mp) cc_final: 0.7625 (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: 0.5233 (mmtp) REVERT: B 296 ASN cc_start: 0.7113 (m-40) cc_final: 0.6911 (m-40) REVERT: B 300 LEU cc_start: 0.8813 (mt) cc_final: 0.8505 (mt) REVERT: B 334 TRP cc_start: 0.8054 (t60) cc_final: 0.7185 (t60) REVERT: B 643 LEU cc_start: 0.7393 (mt) cc_final: 0.7158 (mt) REVERT: B 751 LYS cc_start: 0.5448 (mttt) cc_final: 0.4756 (ttmt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.0980 time to fit residues: 35.1729 Evaluate side-chains 183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 426 HIS 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 426 HIS B 642 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.198087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.161257 restraints weight = 16397.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.165288 restraints weight = 9636.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.167879 restraints weight = 7029.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.169091 restraints weight = 5850.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.169111 restraints weight = 5311.897| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7964 Z= 0.202 Angle : 0.817 9.779 10836 Z= 0.426 Chirality : 0.046 0.217 1250 Planarity : 0.005 0.041 1354 Dihedral : 5.693 25.786 1092 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 2.36 % Allowed : 12.04 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.24), residues: 1004 helix: -1.38 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -4.53 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 617 TYR 0.022 0.002 TYR A 757 PHE 0.024 0.002 PHE A 853 TRP 0.041 0.003 TRP B 427 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7964) covalent geometry : angle 0.81744 (10836) hydrogen bonds : bond 0.07162 ( 417) hydrogen bonds : angle 6.92749 ( 1233) *********************** 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 235 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 CYS cc_start: 0.7602 (m) cc_final: 0.7241 (m) REVERT: A 578 PHE cc_start: 0.7942 (t80) cc_final: 0.7675 (t80) REVERT: A 628 MET cc_start: 0.7778 (tpp) cc_final: 0.7298 (tpp) REVERT: A 704 ILE cc_start: 0.8066 (mt) cc_final: 0.7650 (mt) REVERT: A 751 LYS cc_start: 0.5627 (mttt) cc_final: 0.5123 (mmtp) REVERT: B 319 LEU cc_start: 0.9062 (tp) cc_final: 0.8760 (pt) REVERT: B 378 MET cc_start: 0.2087 (mtp) cc_final: 0.1473 (mtm) REVERT: B 427 TRP cc_start: 0.8131 (t-100) cc_final: 0.7874 (t-100) REVERT: B 574 GLU cc_start: 0.8482 (mp0) cc_final: 0.8149 (mp0) REVERT: B 751 LYS cc_start: 0.5156 (mttt) cc_final: 0.4795 (ttmt) outliers start: 18 outliers final: 5 residues processed: 226 average time/residue: 0.0747 time to fit residues: 23.8154 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 PHE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.195035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.158919 restraints weight = 15733.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.162591 restraints weight = 9597.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.165031 restraints weight = 7104.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.166125 restraints weight = 5937.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.166391 restraints weight = 5402.984| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7964 Z= 0.193 Angle : 0.761 11.109 10836 Z= 0.392 Chirality : 0.045 0.229 1250 Planarity : 0.004 0.036 1354 Dihedral : 5.438 21.537 1092 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 3.93 % Allowed : 15.05 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.25), residues: 1004 helix: -0.77 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -4.43 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 437 TYR 0.013 0.001 TYR A 757 PHE 0.025 0.002 PHE B 581 TRP 0.029 0.002 TRP B 427 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7964) covalent geometry : angle 0.76064 (10836) hydrogen bonds : bond 0.05831 ( 417) hydrogen bonds : angle 6.17865 ( 1233) *********************** 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: 30 poor density : 192 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7894 (tptp) REVERT: A 353 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: A 357 CYS cc_start: 0.7344 (m) cc_final: 0.7118 (m) REVERT: A 427 TRP cc_start: 0.7851 (t-100) cc_final: 0.7526 (t-100) REVERT: A 431 GLN cc_start: 0.7527 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 628 MET cc_start: 0.7595 (tpp) cc_final: 0.7116 (tpp) REVERT: A 638 MET cc_start: 0.5429 (mmt) cc_final: 0.5140 (mmt) REVERT: A 760 LEU cc_start: 0.9001 (tp) cc_final: 0.8643 (tp) REVERT: A 775 ILE cc_start: 0.8439 (tt) cc_final: 0.8113 (mt) REVERT: B 319 LEU cc_start: 0.9061 (tp) cc_final: 0.8663 (pt) REVERT: B 341 MET cc_start: 0.8579 (tpp) cc_final: 0.8315 (tpp) REVERT: B 427 TRP cc_start: 0.8202 (t-100) cc_final: 0.7784 (t-100) REVERT: B 574 GLU cc_start: 0.8430 (mp0) cc_final: 0.8100 (mp0) REVERT: B 628 MET cc_start: 0.8173 (tpp) cc_final: 0.7776 (tpp) REVERT: B 629 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 751 LYS cc_start: 0.5013 (mttt) cc_final: 0.4539 (ttmt) outliers start: 30 outliers final: 17 residues processed: 209 average time/residue: 0.0695 time to fit residues: 20.2776 Evaluate side-chains 183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL 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 627 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL 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 713 VAL Chi-restraints excluded: chain B residue 748 ILE 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 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 97 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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** B 406 ASN B 642 GLN ** B 705 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 = 0.4808 r_free = 0.4808 target = 0.199071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.162637 restraints weight = 16296.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.166569 restraints weight = 9763.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.169115 restraints weight = 7141.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.170107 restraints weight = 5960.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.170908 restraints weight = 5448.460| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7964 Z= 0.149 Angle : 0.686 10.456 10836 Z= 0.353 Chirality : 0.043 0.193 1250 Planarity : 0.004 0.035 1354 Dihedral : 5.068 19.472 1092 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 3.14 % Allowed : 17.93 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.25), residues: 1004 helix: -0.36 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -4.51 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.012 0.001 TYR A 757 PHE 0.018 0.002 PHE A 572 TRP 0.019 0.001 TRP B 305 HIS 0.002 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7964) covalent geometry : angle 0.68575 (10836) hydrogen bonds : bond 0.04943 ( 417) hydrogen bonds : angle 5.60567 ( 1233) *********************** 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 218 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8016 (tptp) REVERT: A 427 TRP cc_start: 0.7799 (t-100) cc_final: 0.7513 (t-100) REVERT: A 628 MET cc_start: 0.7086 (tpp) cc_final: 0.6791 (tpp) REVERT: A 742 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6851 (mm) REVERT: A 760 LEU cc_start: 0.8965 (tp) cc_final: 0.8712 (tp) REVERT: A 782 ILE cc_start: 0.4438 (mt) cc_final: 0.3778 (mm) REVERT: A 797 MET cc_start: 0.1865 (ptm) cc_final: 0.1623 (ptm) REVERT: B 341 MET cc_start: 0.8470 (tpp) cc_final: 0.8212 (tpp) REVERT: B 574 GLU cc_start: 0.8417 (mp0) cc_final: 0.8119 (mp0) REVERT: B 629 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 751 LYS cc_start: 0.4787 (mttt) cc_final: 0.4507 (ttmt) REVERT: B 784 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6788 (tpm170) outliers start: 24 outliers final: 12 residues processed: 206 average time/residue: 0.0678 time to fit residues: 19.7468 Evaluate side-chains 181 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 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 746 VAL Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.0270 chunk 73 optimal weight: 6.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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** ** B 375 ASN ** 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 803 HIS B 820 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.198012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.161750 restraints weight = 16396.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.165545 restraints weight = 9969.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.168080 restraints weight = 7381.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.169236 restraints weight = 6209.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.169509 restraints weight = 5648.612| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.6429 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= 0.149 Angle : 0.682 9.404 10836 Z= 0.350 Chirality : 0.043 0.280 1250 Planarity : 0.004 0.034 1354 Dihedral : 4.896 18.671 1092 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 4.71 % Allowed : 18.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.25), residues: 1004 helix: -0.06 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -4.62 (0.26), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.011 0.001 TYR A 757 PHE 0.035 0.002 PHE A 853 TRP 0.017 0.001 TRP B 305 HIS 0.002 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7964) covalent geometry : angle 0.68238 (10836) hydrogen bonds : bond 0.04632 ( 417) hydrogen bonds : angle 5.35633 ( 1233) *********************** 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 216 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7951 (tptp) REVERT: A 364 ILE cc_start: 0.5710 (mm) cc_final: 0.5430 (tp) REVERT: A 427 TRP cc_start: 0.7804 (t-100) cc_final: 0.7486 (t-100) REVERT: A 628 MET cc_start: 0.7003 (tpp) cc_final: 0.6711 (tpp) REVERT: A 742 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6920 (mm) REVERT: A 760 LEU cc_start: 0.8996 (tp) cc_final: 0.8761 (tp) REVERT: B 335 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8164 (tt) REVERT: B 497 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7460 (tt) REVERT: B 541 ILE cc_start: 0.8755 (pt) cc_final: 0.8514 (pt) REVERT: B 574 GLU cc_start: 0.8381 (mp0) cc_final: 0.8010 (mp0) REVERT: B 628 MET cc_start: 0.8303 (tpp) cc_final: 0.8030 (tpp) REVERT: B 629 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8539 (mm-30) REVERT: B 784 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6767 (tpm170) outliers start: 36 outliers final: 15 residues processed: 202 average time/residue: 0.0641 time to fit residues: 18.6460 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 627 LEU 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 769 ILE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 643 LEU 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 864 VAL Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 809 ASN ** B 375 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.197326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.160574 restraints weight = 16309.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.164257 restraints weight = 10179.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.166749 restraints weight = 7581.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.167817 restraints weight = 6373.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.167885 restraints weight = 5802.465| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7964 Z= 0.158 Angle : 0.694 9.780 10836 Z= 0.352 Chirality : 0.043 0.194 1250 Planarity : 0.004 0.032 1354 Dihedral : 4.843 19.721 1092 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 4.45 % Allowed : 19.63 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.25), residues: 1004 helix: 0.00 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -4.47 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.009 0.001 TYR A 757 PHE 0.025 0.002 PHE A 853 TRP 0.031 0.002 TRP B 419 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7964) covalent geometry : angle 0.69414 (10836) hydrogen bonds : bond 0.04562 ( 417) hydrogen bonds : angle 5.29016 ( 1233) *********************** 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 217 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7956 (tptp) REVERT: A 427 TRP cc_start: 0.7836 (t-100) cc_final: 0.7562 (t-100) REVERT: A 628 MET cc_start: 0.7011 (tpp) cc_final: 0.6773 (tpp) REVERT: A 760 LEU cc_start: 0.9001 (tp) cc_final: 0.8771 (tp) REVERT: A 797 MET cc_start: 0.1842 (ptm) cc_final: 0.1499 (ptp) REVERT: B 335 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8090 (tt) REVERT: B 341 MET cc_start: 0.8522 (tpp) cc_final: 0.8131 (tpp) REVERT: B 541 ILE cc_start: 0.8719 (pt) cc_final: 0.8488 (pt) REVERT: B 574 GLU cc_start: 0.8367 (mp0) cc_final: 0.8010 (mp0) REVERT: B 628 MET cc_start: 0.8186 (tpp) cc_final: 0.7813 (tpp) REVERT: B 629 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8510 (mm-30) REVERT: B 784 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6787 (tpm170) outliers start: 34 outliers final: 23 residues processed: 201 average time/residue: 0.0638 time to fit residues: 18.5690 Evaluate side-chains 196 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 GLU 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 434 LEU 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 713 VAL Chi-restraints excluded: chain A residue 769 ILE 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 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 643 LEU 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 856 VAL Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.0030 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 642 GLN ** A 726 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.201351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.165844 restraints weight = 16307.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.169783 restraints weight = 9891.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.172441 restraints weight = 7273.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.173514 restraints weight = 6043.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.173522 restraints weight = 5503.394| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7964 Z= 0.131 Angle : 0.681 10.684 10836 Z= 0.340 Chirality : 0.042 0.166 1250 Planarity : 0.003 0.035 1354 Dihedral : 4.691 19.128 1092 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.01 % Allowed : 22.25 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.25), residues: 1004 helix: 0.17 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -4.56 (0.26), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.011 0.001 TYR A 757 PHE 0.025 0.002 PHE B 581 TRP 0.017 0.001 TRP B 419 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7964) covalent geometry : angle 0.68062 (10836) hydrogen bonds : bond 0.04201 ( 417) hydrogen bonds : angle 5.11211 ( 1233) *********************** 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 200 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8256 (ttmt) cc_final: 0.8036 (tptp) REVERT: A 427 TRP cc_start: 0.7755 (t-100) cc_final: 0.7425 (t-100) REVERT: A 496 MET cc_start: 0.7001 (pmm) cc_final: 0.6638 (pmm) REVERT: A 782 ILE cc_start: 0.4497 (mt) cc_final: 0.3750 (mm) REVERT: A 797 MET cc_start: 0.1731 (ptm) cc_final: 0.1405 (ptp) REVERT: B 341 MET cc_start: 0.8318 (tpp) cc_final: 0.7981 (tpp) REVERT: B 541 ILE cc_start: 0.8671 (pt) cc_final: 0.8464 (pt) REVERT: B 574 GLU cc_start: 0.8299 (mp0) cc_final: 0.8016 (mp0) REVERT: B 628 MET cc_start: 0.8206 (tpp) cc_final: 0.7903 (tpp) REVERT: B 784 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6723 (tpm170) outliers start: 23 outliers final: 12 residues processed: 191 average time/residue: 0.0805 time to fit residues: 21.7124 Evaluate side-chains 185 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET 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 856 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 820 ASN 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 41 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 642 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 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 = 0.4749 r_free = 0.4749 target = 0.193983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.157815 restraints weight = 16390.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.161306 restraints weight = 10251.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.163434 restraints weight = 7729.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.164469 restraints weight = 6590.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.164681 restraints weight = 6039.551| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7964 Z= 0.206 Angle : 0.755 10.293 10836 Z= 0.386 Chirality : 0.045 0.181 1250 Planarity : 0.004 0.029 1354 Dihedral : 4.904 22.938 1092 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 4.97 % Allowed : 21.34 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.25), residues: 1004 helix: -0.03 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -4.68 (0.26), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 373 TYR 0.017 0.002 TYR A 338 PHE 0.058 0.003 PHE B 412 TRP 0.015 0.002 TRP B 419 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7964) covalent geometry : angle 0.75521 (10836) hydrogen bonds : bond 0.04894 ( 417) hydrogen bonds : angle 5.38754 ( 1233) *********************** 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 212 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8034 (tptp) REVERT: A 353 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: A 399 ARG cc_start: 0.6810 (ptt90) cc_final: 0.5177 (ptm-80) REVERT: A 496 MET cc_start: 0.7496 (pmm) cc_final: 0.7155 (pmm) REVERT: A 782 ILE cc_start: 0.4801 (mt) cc_final: 0.4111 (mm) REVERT: A 797 MET cc_start: 0.1806 (ptm) cc_final: 0.1477 (ptp) REVERT: B 300 LEU cc_start: 0.8029 (pp) cc_final: 0.7429 (mm) REVERT: B 341 MET cc_start: 0.8532 (tpp) cc_final: 0.8279 (tpp) REVERT: B 541 ILE cc_start: 0.8751 (pt) cc_final: 0.8511 (pt) REVERT: B 574 GLU cc_start: 0.8412 (mp0) cc_final: 0.8123 (mp0) REVERT: B 628 MET cc_start: 0.8211 (tpp) cc_final: 0.7923 (tpp) REVERT: B 784 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6823 (tpm170) outliers start: 38 outliers final: 26 residues processed: 198 average time/residue: 0.0749 time to fit residues: 21.3606 Evaluate side-chains 198 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 ILE 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 510 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 769 ILE 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 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 643 LEU 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 856 VAL 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 8 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 642 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 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 = 0.4803 r_free = 0.4803 target = 0.198980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.163612 restraints weight = 15982.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.167417 restraints weight = 9882.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.169950 restraints weight = 7316.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.171083 restraints weight = 6115.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.171533 restraints weight = 5537.823| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7964 Z= 0.143 Angle : 0.744 13.685 10836 Z= 0.363 Chirality : 0.044 0.232 1250 Planarity : 0.004 0.038 1354 Dihedral : 4.811 21.731 1092 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.40 % Allowed : 22.77 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.26), residues: 1004 helix: 0.20 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -4.44 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.020 0.001 TYR B 323 PHE 0.064 0.002 PHE B 412 TRP 0.019 0.002 TRP B 427 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7964) covalent geometry : angle 0.74370 (10836) hydrogen bonds : bond 0.04365 ( 417) hydrogen bonds : angle 5.18173 ( 1233) *********************** 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 205 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8045 (tptp) REVERT: A 399 ARG cc_start: 0.6745 (ptt90) cc_final: 0.5107 (ptm-80) REVERT: A 496 MET cc_start: 0.7340 (pmm) cc_final: 0.7015 (pmm) REVERT: A 797 MET cc_start: 0.1746 (ptm) cc_final: 0.1408 (ptp) REVERT: B 574 GLU cc_start: 0.8382 (mp0) cc_final: 0.8138 (mp0) REVERT: B 628 MET cc_start: 0.7807 (tpp) cc_final: 0.7537 (tpp) REVERT: B 751 LYS cc_start: 0.4489 (ttmt) cc_final: 0.4284 (ttpt) REVERT: B 784 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6606 (tpm170) REVERT: B 797 MET cc_start: 0.0379 (ttt) cc_final: -0.0723 (ptp) outliers start: 26 outliers final: 17 residues processed: 192 average time/residue: 0.0785 time to fit residues: 21.2218 Evaluate side-chains 188 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 769 ILE 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 742 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 642 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 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 = 0.4789 r_free = 0.4789 target = 0.198101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.163104 restraints weight = 16273.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.166747 restraints weight = 10124.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.169270 restraints weight = 7519.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.170329 restraints weight = 6285.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.171376 restraints weight = 5714.120| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7964 Z= 0.147 Angle : 0.752 13.881 10836 Z= 0.368 Chirality : 0.043 0.192 1250 Planarity : 0.004 0.035 1354 Dihedral : 4.719 21.617 1092 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.88 % Allowed : 23.69 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.26), residues: 1004 helix: 0.30 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -4.38 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.016 0.001 TYR A 355 PHE 0.066 0.002 PHE B 412 TRP 0.028 0.002 TRP B 419 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7964) covalent geometry : angle 0.75179 (10836) hydrogen bonds : bond 0.04338 ( 417) hydrogen bonds : angle 5.17423 ( 1233) ********************** 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 200 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8033 (tptp) REVERT: A 399 ARG cc_start: 0.6724 (ptt90) cc_final: 0.5112 (ptm-80) REVERT: A 496 MET cc_start: 0.7459 (pmm) cc_final: 0.7163 (pmm) REVERT: A 505 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6860 (mm) REVERT: A 782 ILE cc_start: 0.4748 (mt) cc_final: 0.4106 (mm) REVERT: A 797 MET cc_start: 0.1829 (ptm) cc_final: 0.1457 (ptp) REVERT: B 300 LEU cc_start: 0.7940 (pp) cc_final: 0.7354 (mm) REVERT: B 335 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 574 GLU cc_start: 0.8424 (mp0) cc_final: 0.8120 (mp0) REVERT: B 628 MET cc_start: 0.7680 (tpp) cc_final: 0.7325 (tpp) REVERT: B 784 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6645 (tpm170) outliers start: 22 outliers final: 18 residues processed: 191 average time/residue: 0.0768 time to fit residues: 20.7058 Evaluate side-chains 194 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 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 335 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- 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 642 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 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 = 0.4811 r_free = 0.4811 target = 0.200563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.165402 restraints weight = 16269.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.169233 restraints weight = 10065.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.171175 restraints weight = 7482.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.173024 restraints weight = 6374.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.173746 restraints weight = 5741.895| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7964 Z= 0.136 Angle : 0.743 13.372 10836 Z= 0.363 Chirality : 0.043 0.197 1250 Planarity : 0.003 0.030 1354 Dihedral : 4.631 20.493 1092 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.14 % Allowed : 23.95 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.27), residues: 1004 helix: 0.51 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -4.28 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.019 0.001 TYR A 355 PHE 0.038 0.002 PHE A 722 TRP 0.031 0.002 TRP B 419 HIS 0.003 0.001 HIS B 798 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7964) covalent geometry : angle 0.74284 (10836) hydrogen bonds : bond 0.04117 ( 417) hydrogen bonds : angle 5.04998 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.01 seconds wall clock time: 24 minutes 17.57 seconds (1457.57 seconds total)