Starting phenix.real_space_refine on Mon Mar 11 08:40:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_7095_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_7095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_7095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_7095_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgi_7095/03_2024/6bgi_7095_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 50 5.16 5 C 5120 2.51 5 N 1266 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3885 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 20, 'TRANS': 489} Chain breaks: 3 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3885 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 20, 'TRANS': 489} Chain breaks: 3 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.64, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 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: 1.99 Time building geometry restraints manager: 3.48 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: 98.09 - 105.27: 155 105.27 - 112.45: 4050 112.45 - 119.62: 2661 119.62 - 126.80: 3870 126.80 - 133.98: 100 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 2.440 nonbonded pdb=" O VAL B 586 " pdb=" OG1 THR B 590 " model vdw 2.047 2.440 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 2.440 ... (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 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: 1.640 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: 0.000 Extract box with map and model: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.570 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 7964 Z= 0.490 Angle : 0.999 10.144 10836 Z= 0.578 Chirality : 0.049 0.142 1250 Planarity : 0.005 0.049 1354 Dihedral : 8.911 42.252 2712 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 48.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.14 % Favored : 83.86 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.22), residues: 1004 helix: -3.29 (0.15), residues: 610 sheet: None (None), residues: 0 loop : -3.70 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 854 HIS 0.008 0.002 HIS A 803 PHE 0.046 0.004 PHE A 708 TYR 0.019 0.002 TYR B 589 ARG 0.008 0.001 ARG A 860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TRP cc_start: 0.7904 (t60) cc_final: 0.7059 (t60) REVERT: A 391 MET cc_start: 0.6009 (mtp) cc_final: 0.5742 (mtp) REVERT: A 427 TRP cc_start: 0.7611 (t-100) cc_final: 0.7386 (t-100) REVERT: A 543 LEU cc_start: 0.7956 (mp) cc_final: 0.7626 (mp) REVERT: A 639 LEU cc_start: 0.6946 (mt) cc_final: 0.6343 (mt) REVERT: A 751 LYS cc_start: 0.5630 (mttt) cc_final: 0.5238 (mmtp) REVERT: B 296 ASN cc_start: 0.7113 (m-40) cc_final: 0.6908 (m-40) REVERT: B 300 LEU cc_start: 0.8813 (mt) cc_final: 0.8507 (mt) REVERT: B 334 TRP cc_start: 0.8054 (t60) cc_final: 0.7191 (t60) REVERT: B 643 LEU cc_start: 0.7393 (mt) cc_final: 0.7164 (mt) REVERT: B 751 LYS cc_start: 0.5448 (mttt) cc_final: 0.4765 (ttmt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2384 time to fit residues: 84.5219 Evaluate side-chains 178 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 431 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7964 Z= 0.273 Angle : 0.787 8.371 10836 Z= 0.412 Chirality : 0.046 0.224 1250 Planarity : 0.005 0.040 1354 Dihedral : 5.755 25.607 1092 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 3.27 % Allowed : 10.73 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.24), residues: 1004 helix: -1.47 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -4.50 (0.27), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 427 HIS 0.005 0.001 HIS B 402 PHE 0.022 0.002 PHE A 853 TYR 0.021 0.002 TYR A 757 ARG 0.009 0.001 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 CYS cc_start: 0.7553 (m) cc_final: 0.7002 (m) REVERT: A 578 PHE cc_start: 0.7780 (t80) cc_final: 0.7473 (t80) REVERT: A 628 MET cc_start: 0.7825 (tpp) cc_final: 0.7523 (tpp) REVERT: A 704 ILE cc_start: 0.7900 (mt) cc_final: 0.7436 (mt) REVERT: B 378 MET cc_start: 0.2709 (mtp) cc_final: 0.1890 (mtm) outliers start: 25 outliers final: 13 residues processed: 230 average time/residue: 0.1852 time to fit residues: 59.4361 Evaluate side-chains 191 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 HIS ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 HIS ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7964 Z= 0.246 Angle : 0.737 11.473 10836 Z= 0.377 Chirality : 0.044 0.190 1250 Planarity : 0.004 0.037 1354 Dihedral : 5.254 19.994 1092 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 4.06 % Allowed : 14.79 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.25), residues: 1004 helix: -0.93 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -4.50 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 427 HIS 0.003 0.001 HIS B 426 PHE 0.024 0.002 PHE B 581 TYR 0.021 0.001 TYR A 594 ARG 0.006 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TRP cc_start: 0.7471 (t-100) cc_final: 0.7259 (t-100) REVERT: A 578 PHE cc_start: 0.7736 (t80) cc_final: 0.7491 (t80) REVERT: A 628 MET cc_start: 0.7332 (tpp) cc_final: 0.6790 (tpp) REVERT: A 760 LEU cc_start: 0.9001 (tp) cc_final: 0.8729 (tp) REVERT: A 775 ILE cc_start: 0.8334 (tt) cc_final: 0.7965 (mt) REVERT: B 574 GLU cc_start: 0.8269 (mp0) cc_final: 0.7993 (mp0) REVERT: B 628 MET cc_start: 0.8062 (tpp) cc_final: 0.7841 (tpp) REVERT: B 629 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 751 LYS cc_start: 0.5675 (ttmt) cc_final: 0.5386 (ttmt) outliers start: 31 outliers final: 20 residues processed: 218 average time/residue: 0.1632 time to fit residues: 50.2267 Evaluate side-chains 190 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 THR 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 742 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 50.0000 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7964 Z= 0.296 Angle : 0.754 10.662 10836 Z= 0.393 Chirality : 0.045 0.226 1250 Planarity : 0.004 0.040 1354 Dihedral : 5.277 21.304 1092 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 5.37 % Allowed : 16.75 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.25), residues: 1004 helix: -0.65 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -4.62 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 427 HIS 0.002 0.001 HIS B 426 PHE 0.021 0.002 PHE B 581 TYR 0.014 0.001 TYR B 374 ARG 0.005 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7925 (tptp) REVERT: A 353 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: A 399 ARG cc_start: 0.6630 (ttt-90) cc_final: 0.6215 (ttp80) REVERT: A 427 TRP cc_start: 0.7682 (t-100) cc_final: 0.7426 (t-100) REVERT: A 628 MET cc_start: 0.6870 (tpp) cc_final: 0.6403 (tpp) REVERT: A 638 MET cc_start: 0.5221 (mmt) cc_final: 0.4933 (mmt) REVERT: A 742 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6723 (mm) REVERT: A 797 MET cc_start: 0.2256 (ptm) cc_final: 0.2048 (ptm) REVERT: B 300 LEU cc_start: 0.8007 (pp) cc_final: 0.7678 (mm) REVERT: B 574 GLU cc_start: 0.8390 (mp0) cc_final: 0.8061 (mp0) outliers start: 41 outliers final: 31 residues processed: 200 average time/residue: 0.1752 time to fit residues: 48.6954 Evaluate side-chains 195 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 chunk 19 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 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 406 ASN B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.6297 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= 0.218 Angle : 0.684 10.352 10836 Z= 0.352 Chirality : 0.043 0.198 1250 Planarity : 0.004 0.034 1354 Dihedral : 5.026 20.074 1092 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 5.63 % Allowed : 17.41 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.25), residues: 1004 helix: -0.34 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -4.48 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 427 HIS 0.003 0.001 HIS B 426 PHE 0.033 0.002 PHE B 581 TYR 0.011 0.001 TYR A 757 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7943 (tptp) REVERT: A 353 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: A 399 ARG cc_start: 0.6527 (ttt-90) cc_final: 0.5465 (ptm-80) REVERT: A 578 PHE cc_start: 0.7879 (t80) cc_final: 0.7473 (t80) REVERT: A 628 MET cc_start: 0.6953 (tpp) cc_final: 0.6631 (tpp) REVERT: A 742 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 782 ILE cc_start: 0.4640 (mt) cc_final: 0.4018 (mm) REVERT: B 378 MET cc_start: 0.1512 (mtp) cc_final: 0.1236 (mtp) REVERT: B 574 GLU cc_start: 0.8324 (mp0) cc_final: 0.7989 (mp0) REVERT: B 628 MET cc_start: 0.7524 (tpp) cc_final: 0.7158 (tpp) REVERT: B 784 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6755 (tpm170) outliers start: 43 outliers final: 23 residues processed: 209 average time/residue: 0.1701 time to fit residues: 49.5923 Evaluate side-chains 195 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 422 THR 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 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7964 Z= 0.218 Angle : 0.707 10.074 10836 Z= 0.358 Chirality : 0.045 0.299 1250 Planarity : 0.004 0.031 1354 Dihedral : 4.899 20.602 1092 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 5.63 % Allowed : 18.85 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.25), residues: 1004 helix: -0.25 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -4.45 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 427 HIS 0.004 0.001 HIS B 798 PHE 0.023 0.002 PHE A 324 TYR 0.009 0.001 TYR A 757 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7969 (tptp) REVERT: A 353 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: A 578 PHE cc_start: 0.7963 (t80) cc_final: 0.7524 (t80) REVERT: A 742 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6879 (mm) REVERT: A 797 MET cc_start: 0.2182 (ptm) cc_final: 0.1816 (ptp) REVERT: B 300 LEU cc_start: 0.8126 (pp) cc_final: 0.7544 (mm) REVERT: B 342 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7472 (tt) REVERT: B 378 MET cc_start: 0.1782 (mtp) cc_final: 0.1292 (mtp) REVERT: B 541 ILE cc_start: 0.8715 (pt) cc_final: 0.8460 (pt) REVERT: B 574 GLU cc_start: 0.8304 (mp0) cc_final: 0.7962 (mp0) REVERT: B 628 MET cc_start: 0.7520 (tpp) cc_final: 0.7113 (tpp) REVERT: B 784 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6835 (tpm170) outliers start: 43 outliers final: 29 residues processed: 204 average time/residue: 0.2047 time to fit residues: 57.8673 Evaluate side-chains 202 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 THR 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 713 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 588 SER 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 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.0010 chunk 58 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7964 Z= 0.183 Angle : 0.693 12.348 10836 Z= 0.344 Chirality : 0.043 0.234 1250 Planarity : 0.004 0.029 1354 Dihedral : 4.720 18.445 1092 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.93 % Allowed : 20.94 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.25), residues: 1004 helix: -0.03 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.77 (0.25), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 427 HIS 0.004 0.001 HIS B 798 PHE 0.023 0.001 PHE A 324 TYR 0.023 0.001 TYR A 355 ARG 0.004 0.000 ARG B 749 *********************** 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 214 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8017 (tptp) REVERT: A 399 ARG cc_start: 0.6971 (ptt90) cc_final: 0.5360 (ptm-80) REVERT: A 578 PHE cc_start: 0.7965 (t80) cc_final: 0.7545 (t80) REVERT: A 776 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7432 (t) REVERT: A 797 MET cc_start: 0.2151 (ptm) cc_final: 0.1787 (ptp) REVERT: B 378 MET cc_start: 0.0928 (mtp) cc_final: 0.0475 (mtp) REVERT: B 541 ILE cc_start: 0.8635 (pt) cc_final: 0.8377 (pt) REVERT: B 574 GLU cc_start: 0.8227 (mp0) cc_final: 0.7936 (mp0) REVERT: B 628 MET cc_start: 0.7482 (tpp) cc_final: 0.7126 (tpp) REVERT: B 751 LYS cc_start: 0.4574 (ttmt) cc_final: 0.4161 (ttpt) REVERT: B 784 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6710 (tpm170) outliers start: 30 outliers final: 20 residues processed: 202 average time/residue: 0.1638 time to fit residues: 46.5005 Evaluate side-chains 194 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 875 SER 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 588 SER Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 864 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7964 Z= 0.209 Angle : 0.695 12.565 10836 Z= 0.346 Chirality : 0.043 0.249 1250 Planarity : 0.004 0.033 1354 Dihedral : 4.692 19.230 1092 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 3.93 % Allowed : 21.73 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.25), residues: 1004 helix: 0.07 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.72 (0.25), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP A 427 HIS 0.003 0.001 HIS B 798 PHE 0.023 0.002 PHE B 581 TYR 0.017 0.001 TYR A 355 ARG 0.005 0.000 ARG A 761 *********************** 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 209 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8032 (tptp) REVERT: A 399 ARG cc_start: 0.6903 (ptt90) cc_final: 0.5371 (ptm-80) REVERT: A 628 MET cc_start: 0.7965 (tpp) cc_final: 0.7517 (tpp) REVERT: A 776 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7619 (t) REVERT: A 782 ILE cc_start: 0.4784 (mt) cc_final: 0.4196 (mm) REVERT: A 797 MET cc_start: 0.2188 (ptm) cc_final: 0.1821 (ptp) REVERT: B 342 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7482 (tt) REVERT: B 378 MET cc_start: 0.0908 (mtp) cc_final: 0.0469 (mtp) REVERT: B 541 ILE cc_start: 0.8636 (pt) cc_final: 0.8369 (pt) REVERT: B 628 MET cc_start: 0.7364 (tpp) cc_final: 0.6998 (tpp) REVERT: B 784 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6631 (tpm170) outliers start: 30 outliers final: 25 residues processed: 198 average time/residue: 0.1680 time to fit residues: 46.6505 Evaluate side-chains 198 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7964 Z= 0.227 Angle : 0.723 12.116 10836 Z= 0.362 Chirality : 0.044 0.237 1250 Planarity : 0.004 0.037 1354 Dihedral : 4.740 19.895 1092 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 4.45 % Allowed : 21.20 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.26), residues: 1004 helix: 0.11 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.66 (0.26), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP A 427 HIS 0.003 0.001 HIS B 798 PHE 0.023 0.002 PHE A 722 TYR 0.017 0.001 TYR A 355 ARG 0.005 0.000 ARG B 749 *********************** 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 203 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8008 (tptp) REVERT: A 334 TRP cc_start: 0.7773 (t60) cc_final: 0.7333 (t60) REVERT: A 399 ARG cc_start: 0.6848 (ptt90) cc_final: 0.5324 (ptm-80) REVERT: A 628 MET cc_start: 0.7988 (tpp) cc_final: 0.7467 (tpp) REVERT: A 776 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 782 ILE cc_start: 0.4638 (mt) cc_final: 0.3959 (mm) REVERT: A 797 MET cc_start: 0.2250 (ptm) cc_final: 0.1871 (ptp) REVERT: B 334 TRP cc_start: 0.8487 (t60) cc_final: 0.7853 (t-100) REVERT: B 342 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7809 (tt) REVERT: B 378 MET cc_start: 0.0953 (mtp) cc_final: 0.0512 (mtp) REVERT: B 427 TRP cc_start: 0.7565 (t-100) cc_final: 0.7238 (t-100) REVERT: B 541 ILE cc_start: 0.8701 (pt) cc_final: 0.8448 (pt) REVERT: B 628 MET cc_start: 0.7396 (tpp) cc_final: 0.7087 (tpp) REVERT: B 784 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6774 (tpm170) outliers start: 34 outliers final: 28 residues processed: 190 average time/residue: 0.1694 time to fit residues: 44.7226 Evaluate side-chains 197 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.7507 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= 0.198 Angle : 0.729 12.339 10836 Z= 0.361 Chirality : 0.044 0.245 1250 Planarity : 0.004 0.038 1354 Dihedral : 4.678 19.233 1092 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 3.80 % Allowed : 22.25 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.26), residues: 1004 helix: 0.17 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.69 (0.26), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.003 TRP A 427 HIS 0.003 0.001 HIS B 798 PHE 0.022 0.002 PHE A 324 TYR 0.019 0.001 TYR A 355 ARG 0.004 0.000 ARG A 761 ********************** 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 207 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8014 (tptp) REVERT: A 399 ARG cc_start: 0.6832 (ptt90) cc_final: 0.5279 (ptm-80) REVERT: A 628 MET cc_start: 0.7949 (tpp) cc_final: 0.7391 (tpp) REVERT: A 776 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 797 MET cc_start: 0.2183 (ptm) cc_final: 0.1817 (ptp) REVERT: B 378 MET cc_start: 0.0580 (mtp) cc_final: 0.0149 (mtp) REVERT: B 427 TRP cc_start: 0.7469 (t-100) cc_final: 0.7163 (t-100) REVERT: B 428 LYS cc_start: 0.7929 (tptp) cc_final: 0.7714 (ttpt) REVERT: B 628 MET cc_start: 0.7429 (tpp) cc_final: 0.7036 (tpp) REVERT: B 700 MET cc_start: 0.7754 (ttm) cc_final: 0.7344 (ttm) REVERT: B 749 ARG cc_start: 0.4092 (mmt180) cc_final: 0.3869 (mmt180) REVERT: B 776 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7410 (t) REVERT: B 784 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6662 (tpm170) outliers start: 29 outliers final: 21 residues processed: 197 average time/residue: 0.1828 time to fit residues: 49.7815 Evaluate side-chains 191 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 820 ASN 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 434 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 784 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 ASN Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** 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 = 0.4779 r_free = 0.4779 target = 0.196153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.160398 restraints weight = 16045.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.164037 restraints weight = 9933.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.166441 restraints weight = 7348.225| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7964 Z= 0.216 Angle : 0.749 12.323 10836 Z= 0.367 Chirality : 0.044 0.239 1250 Planarity : 0.004 0.031 1354 Dihedral : 4.646 20.142 1092 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 4.06 % Allowed : 22.38 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.26), residues: 1004 helix: 0.24 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.64 (0.26), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP A 427 HIS 0.003 0.001 HIS B 798 PHE 0.035 0.002 PHE A 722 TYR 0.031 0.001 TYR B 323 ARG 0.003 0.000 ARG A 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.45 seconds wall clock time: 34 minutes 26.34 seconds (2066.34 seconds total)