Starting phenix.real_space_refine on Tue May 5 00:49:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.map" model { file = "/net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jre_61752/05_2026/9jre_61752.cif" } resolution = 4.1 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= 0.021 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: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 15652 2.51 5 N 4215 2.21 5 O 4598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24598 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6215 Classifications: {'peptide': 788} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 760} Chain breaks: 2 Chain: "B" Number of atoms: 6035 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 767, 6024 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 739} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 767, 6024 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 739} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6135 Chain: "C" Number of atoms: 6103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 6092 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 748} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 776, 6092 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 748} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6203 Chain: "D" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6245 Classifications: {'peptide': 793} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 765} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG B 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG B 226 " occ=0.48 residue: pdb=" N AARG C 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG C 226 " occ=0.48 Time building chain proxies: 8.48, per 1000 atoms: 0.34 Number of scatterers: 24598 At special positions: 0 Unit cell: (165.98, 145.34, 196.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 4598 8.00 N 4215 7.00 C 15652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 128 " distance=2.04 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 128 " distance=2.04 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 128 " distance=2.04 Simple disulfide: pdb=" SG CYS D 294 " - pdb=" SG CYS D 306 " distance=2.04 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5882 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 25 sheets defined 48.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 52 Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.503A pdb=" N THR A 84 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.519A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.547A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.550A pdb=" N ASP A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 340 Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.590A pdb=" N SER A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 4.380A pdb=" N PHE A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 587 removed outlier: 4.340A pdb=" N TRP A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 628 through 660 removed outlier: 3.772A pdb=" N ILE A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 649 " --> pdb=" O CYS A 645 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 658 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.708A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.849A pdb=" N THR A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.553A pdb=" N ALA A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.560A pdb=" N GLY A 716 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 718 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.665A pdb=" N GLY A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.510A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 794 removed outlier: 4.661A pdb=" N PHE A 784 " --> pdb=" O TYR A 780 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 802 removed outlier: 3.802A pdb=" N VAL A 799 " --> pdb=" O GLY A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 831 through 855 removed outlier: 3.902A pdb=" N PHE A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.676A pdb=" N LEU B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.996A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 317 through 340 Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.512A pdb=" N MET B 451 " --> pdb=" O PRO B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.585A pdb=" N ASP B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.681A pdb=" N LEU B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 509 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 511 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.957A pdb=" N LEU B 557 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 587 removed outlier: 3.577A pdb=" N TRP B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Proline residue: B 574 - end of helix Processing helix chain 'B' and resid 628 through 661 removed outlier: 4.452A pdb=" N SER B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TRP B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 649 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 661 " --> pdb=" O THR B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 702 through 712 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.613A pdb=" N LYS B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 734 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 780 through 795 removed outlier: 3.622A pdb=" N GLY B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 Processing helix chain 'B' and resid 812 through 817 removed outlier: 3.542A pdb=" N SER B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.763A pdb=" N THR B 821 " --> pdb=" O SER B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 857 removed outlier: 4.479A pdb=" N GLY B 833 " --> pdb=" O HIS B 829 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP B 855 " --> pdb=" O LEU B 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.676A pdb=" N LEU C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 148 through 160 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 200 through 212 removed outlier: 3.996A pdb=" N PHE C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 317 through 340 Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.668A pdb=" N LEU C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 523 through 528 removed outlier: 3.938A pdb=" N SER C 528 " --> pdb=" O PRO C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 removed outlier: 3.832A pdb=" N PHE C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 590 removed outlier: 4.343A pdb=" N TRP C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 567 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Proline residue: C 574 - end of helix Processing helix chain 'C' and resid 627 through 661 removed outlier: 3.742A pdb=" N ARG C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET C 661 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 removed outlier: 3.938A pdb=" N GLN C 674 " --> pdb=" O ASP C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 693 removed outlier: 3.847A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 696 No H-bonds generated for 'chain 'C' and resid 694 through 696' Processing helix chain 'C' and resid 702 through 717 removed outlier: 5.697A pdb=" N LYS C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN C 715 " --> pdb=" O THR C 711 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 removed outlier: 4.158A pdb=" N ARG C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS C 731 " --> pdb=" O GLU C 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 731' Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 778 through 792 removed outlier: 4.457A pdb=" N ASP C 782 " --> pdb=" O SER C 778 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 783 " --> pdb=" O PRO C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 805 removed outlier: 3.939A pdb=" N VAL C 799 " --> pdb=" O GLY C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 819 removed outlier: 3.605A pdb=" N SER C 817 " --> pdb=" O LEU C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 857 removed outlier: 4.009A pdb=" N PHE C 831 " --> pdb=" O LYS C 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 52 Processing helix chain 'D' and resid 71 through 85 removed outlier: 3.503A pdb=" N THR D 84 " --> pdb=" O CYS D 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.519A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.549A pdb=" N VAL D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.552A pdb=" N ASP D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 317 through 340 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 454 through 459 removed outlier: 4.383A pdb=" N GLY D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN D 459 " --> pdb=" O ASN D 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 459' Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.621A pdb=" N LEU D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.807A pdb=" N LEU D 508 " --> pdb=" O MET D 504 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 530 Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.511A pdb=" N PHE D 558 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 589 Proline residue: D 574 - end of helix Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.926A pdb=" N ARG D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 662 removed outlier: 4.459A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR D 649 " --> pdb=" O CYS D 645 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 662 " --> pdb=" O VAL D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 removed outlier: 4.201A pdb=" N SER D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 702 through 714 removed outlier: 4.339A pdb=" N ALA D 706 " --> pdb=" O ASP D 702 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 780 through 795 Processing helix chain 'D' and resid 795 through 805 removed outlier: 3.565A pdb=" N TRP D 805 " --> pdb=" O LYS D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 857 removed outlier: 3.580A pdb=" N PHE D 831 " --> pdb=" O LYS D 827 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY D 833 " --> pdb=" O HIS D 829 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL D 834 " --> pdb=" O SER D 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.121A pdb=" N ILE A 24 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER A 63 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 26 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS A 65 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA A 28 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE A 67 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 30 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL A 91 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 27 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER A 93 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 29 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS A 113 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 196 removed outlier: 7.516A pdb=" N LYS A 164 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE A 228 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 166 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A 230 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 168 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A 278 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 398 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS A 411 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR A 400 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N MET A 409 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N SER A 402 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS A 407 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 Processing sheet with id=AA5, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.018A pdb=" N TYR A 770 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.688A pdb=" N PHE A 739 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 541 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 763 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 543 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE B 24 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 63 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 26 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS B 65 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 28 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 67 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 30 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL B 91 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 27 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER B 93 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 29 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 90 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 116 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS B 113 " --> pdb=" O LEU B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 191 through 197 removed outlier: 7.339A pdb=" N LYS B 164 " --> pdb=" O AARG B 226 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE B 228 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 166 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 230 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 168 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY B 398 " --> pdb=" O LYS B 411 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS B 411 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 442 removed outlier: 6.604A pdb=" N LYS B 440 " --> pdb=" O LEU B 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 537 through 538 removed outlier: 4.112A pdb=" N MET B 537 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.818A pdb=" N TRP B 741 " --> pdb=" O GLY B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE C 24 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER C 63 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 26 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LYS C 65 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 28 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 67 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE C 30 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL C 91 " --> pdb=" O HIS C 25 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY C 27 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER C 93 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 29 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C 90 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL C 116 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR C 92 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS C 113 " --> pdb=" O LEU C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 191 through 197 removed outlier: 7.337A pdb=" N LYS C 164 " --> pdb=" O AARG C 226 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE C 228 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 166 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 230 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C 168 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C 398 " --> pdb=" O LYS C 411 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS C 411 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 373 through 376 Processing sheet with id=AB9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC1, first strand: chain 'C' and resid 740 through 742 Processing sheet with id=AC2, first strand: chain 'D' and resid 59 through 67 removed outlier: 6.121A pdb=" N ILE D 24 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER D 63 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE D 26 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS D 65 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 28 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE D 67 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE D 30 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N VAL D 91 " --> pdb=" O HIS D 25 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 27 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER D 93 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE D 29 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS D 113 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 191 through 196 removed outlier: 7.516A pdb=" N LYS D 164 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE D 228 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 166 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU D 230 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE D 168 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET D 278 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY D 398 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS D 411 " --> pdb=" O GLY D 398 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 400 " --> pdb=" O MET D 409 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET D 409 " --> pdb=" O THR D 400 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER D 402 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS D 407 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AC5, first strand: chain 'D' and resid 373 through 376 Processing sheet with id=AC6, first strand: chain 'D' and resid 484 through 486 removed outlier: 5.832A pdb=" N VAL D 441 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 442 " --> pdb=" O ILE D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 739 through 742 removed outlier: 3.651A pdb=" N TRP D 741 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE D 543 " --> pdb=" O ILE D 761 " (cutoff:3.500A) 1107 hydrogen bonds defined for protein. 3218 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: 4.71 Time building geometry restraints manager: 2.71 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: 8007 1.34 - 1.46: 5799 1.46 - 1.58: 11086 1.58 - 1.71: 0 1.71 - 1.83: 212 Bond restraints: 25104 Sorted by residual: bond pdb=" CA THR C 140 " pdb=" CB THR C 140 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.35e-02 5.49e+03 3.33e+00 bond pdb=" CA THR B 140 " pdb=" CB THR B 140 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.35e-02 5.49e+03 3.08e+00 bond pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 1.542 1.564 -0.022 1.28e-02 6.10e+03 2.84e+00 bond pdb=" CA ALA B 75 " pdb=" CB ALA B 75 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.56e-02 4.11e+03 2.58e+00 bond pdb=" CA ALA C 75 " pdb=" CB ALA C 75 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.56e-02 4.11e+03 2.57e+00 ... (remaining 25099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 32791 1.95 - 3.91: 1085 3.91 - 5.86: 123 5.86 - 7.81: 10 7.81 - 9.77: 2 Bond angle restraints: 34011 Sorted by residual: angle pdb=" N ARG C 353 " pdb=" CA ARG C 353 " pdb=" C ARG C 353 " ideal model delta sigma weight residual 111.82 121.59 -9.77 1.16e+00 7.43e-01 7.09e+01 angle pdb=" N ARG B 353 " pdb=" CA ARG B 353 " pdb=" C ARG B 353 " ideal model delta sigma weight residual 111.82 121.49 -9.67 1.16e+00 7.43e-01 6.95e+01 angle pdb=" N ILE C 352 " pdb=" CA ILE C 352 " pdb=" C ILE C 352 " ideal model delta sigma weight residual 110.72 116.16 -5.44 1.01e+00 9.80e-01 2.90e+01 angle pdb=" N ILE B 352 " pdb=" CA ILE B 352 " pdb=" C ILE B 352 " ideal model delta sigma weight residual 110.72 116.10 -5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" N VAL C 204 " pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 110.30 115.08 -4.78 9.70e-01 1.06e+00 2.43e+01 ... (remaining 34006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13998 17.74 - 35.47: 879 35.47 - 53.21: 174 53.21 - 70.94: 18 70.94 - 88.68: 6 Dihedral angle restraints: 15075 sinusoidal: 5989 harmonic: 9086 Sorted by residual: dihedral pdb=" CB CYS B 756 " pdb=" SG CYS B 756 " pdb=" SG CYS B 811 " pdb=" CB CYS B 811 " ideal model delta sinusoidal sigma weight residual -86.00 -140.13 54.13 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS D 756 " pdb=" SG CYS D 756 " pdb=" SG CYS D 811 " pdb=" CB CYS D 811 " ideal model delta sinusoidal sigma weight residual -86.00 -37.05 -48.95 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS D 80 " pdb=" SG CYS D 80 " pdb=" SG CYS D 351 " pdb=" CB CYS D 351 " ideal model delta sinusoidal sigma weight residual -86.00 -124.15 38.15 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 15072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3106 0.050 - 0.099: 577 0.099 - 0.149: 161 0.149 - 0.198: 11 0.198 - 0.248: 7 Chirality restraints: 3862 Sorted by residual: chirality pdb=" CA ILE D 24 " pdb=" N ILE D 24 " pdb=" C ILE D 24 " pdb=" CB ILE D 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG C 353 " pdb=" N ARG C 353 " pdb=" C ARG C 353 " pdb=" CB ARG C 353 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 3859 not shown) Planarity restraints: 4325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 487 " -0.065 5.00e-02 4.00e+02 9.98e-02 1.60e+01 pdb=" N PRO B 488 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 488 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 488 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 523 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO B 524 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 709 " -0.017 2.00e-02 2.50e+03 1.60e-02 6.38e+00 pdb=" CG TRP C 709 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 709 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 709 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 709 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 709 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 709 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 709 " 0.001 2.00e-02 2.50e+03 ... (remaining 4322 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 329 2.66 - 3.22: 24001 3.22 - 3.78: 37260 3.78 - 4.34: 51216 4.34 - 4.90: 80408 Nonbonded interactions: 193214 Sorted by model distance: nonbonded pdb=" OH TYR C 688 " pdb=" O GLY C 716 " model vdw 2.101 3.040 nonbonded pdb=" NZ LYS C 547 " pdb=" O PRO C 548 " model vdw 2.153 3.120 nonbonded pdb=" OG SER D 678 " pdb=" O ASN D 736 " model vdw 2.157 3.040 nonbonded pdb=" O ALA B 749 " pdb=" OG1 THR B 752 " model vdw 2.168 3.040 nonbonded pdb=" O LEU C 708 " pdb=" OG1 THR C 711 " model vdw 2.170 3.040 ... (remaining 193209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 435 throu \ gh 855)) selection = (chain 'B' and (resid 22 through 225 or resid 227 through 424 or resid 435 throu \ gh 855)) selection = (chain 'C' and (resid 22 through 225 or resid 227 through 424 or resid 435 throu \ gh 587 or resid 627 through 855)) selection = (chain 'D' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 435 throu \ gh 587 or resid 627 through 855)) } 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=0.48 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: 6.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3526 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 : 0.004 0.054 25118 Z= 0.265 Angle : 0.846 26.618 34039 Z= 0.532 Chirality : 0.044 0.248 3862 Planarity : 0.004 0.100 4325 Dihedral : 12.017 88.681 9151 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 0.96 % Allowed : 1.26 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.63 (0.14), residues: 3094 helix: 0.27 (0.13), residues: 1362 sheet: -0.96 (0.24), residues: 365 loop : -0.86 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 660 TYR 0.025 0.002 TYR C 536 PHE 0.015 0.002 PHE A 739 TRP 0.043 0.001 TRP C 709 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00428 (25104) covalent geometry : angle 0.81327 (34011) SS BOND : bond 0.00827 ( 14) SS BOND : angle 8.15934 ( 28) hydrogen bonds : bond 0.18604 ( 1107) hydrogen bonds : angle 6.20786 ( 3218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 459 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.3333 (m-30) cc_final: 0.2706 (t70) REVERT: A 291 ASN cc_start: 0.1874 (OUTLIER) cc_final: 0.1340 (p0) REVERT: A 346 MET cc_start: 0.0018 (tpt) cc_final: -0.0372 (tpt) REVERT: A 699 LEU cc_start: 0.6397 (mt) cc_final: 0.6139 (pt) REVERT: A 705 PHE cc_start: 0.6089 (m-80) cc_final: 0.5829 (m-80) REVERT: B 373 HIS cc_start: 0.3197 (OUTLIER) cc_final: 0.0906 (m-70) REVERT: B 381 MET cc_start: -0.3428 (ttm) cc_final: -0.4413 (tpp) REVERT: B 449 PHE cc_start: 0.6393 (m-80) cc_final: 0.5977 (m-80) REVERT: B 451 MET cc_start: 0.5031 (ptp) cc_final: 0.4389 (mmp) REVERT: B 557 LEU cc_start: 0.8215 (mt) cc_final: 0.7835 (pt) REVERT: B 774 LEU cc_start: 0.8551 (tp) cc_final: 0.8243 (mm) REVERT: C 109 MET cc_start: 0.4246 (mmt) cc_final: 0.1856 (ptt) REVERT: C 677 MET cc_start: 0.5459 (tpt) cc_final: 0.5193 (mmm) REVERT: D 446 GLU cc_start: 0.4331 (mm-30) cc_final: 0.4063 (mm-30) REVERT: D 781 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.8307 (tmt170) REVERT: D 782 ASP cc_start: 0.8084 (p0) cc_final: 0.7644 (t0) outliers start: 26 outliers final: 2 residues processed: 481 average time/residue: 0.1836 time to fit residues: 133.8000 Evaluate side-chains 255 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 203 HIS A 272 HIS A 283 GLN A 291 ASN A 663 ASN A 674 GLN C 455 ASN ** C 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 179 GLN D 200 ASN D 241 ASN D 283 GLN D 373 HIS D 435 GLN D 715 ASN D 736 ASN ** D 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.162633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.152698 restraints weight = 183065.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.152634 restraints weight = 151001.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.151442 restraints weight = 128574.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.150937 restraints weight = 135692.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.150119 restraints weight = 123357.159| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4583 r_free = 0.4583 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4583 r_free = 0.4583 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4647 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25118 Z= 0.229 Angle : 0.747 11.115 34039 Z= 0.394 Chirality : 0.048 0.309 3862 Planarity : 0.006 0.088 4325 Dihedral : 5.188 29.990 3363 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.22 % Allowed : 3.66 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.51 (0.15), residues: 3094 helix: 0.39 (0.13), residues: 1404 sheet: -0.75 (0.24), residues: 403 loop : -0.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 155 TYR 0.032 0.003 TYR B 690 PHE 0.028 0.003 PHE B 739 TRP 0.028 0.002 TRP C 501 HIS 0.010 0.002 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00505 (25104) covalent geometry : angle 0.74637 (34011) SS BOND : bond 0.00712 ( 14) SS BOND : angle 1.57478 ( 28) hydrogen bonds : bond 0.06088 ( 1107) hydrogen bonds : angle 5.21745 ( 3218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 276 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.1073 (mt) cc_final: 0.0793 (mt) REVERT: A 295 MET cc_start: 0.2056 (mmt) cc_final: 0.0512 (mmp) REVERT: A 315 MET cc_start: 0.2454 (tmm) cc_final: 0.2210 (tpp) REVERT: A 381 MET cc_start: 0.0011 (mtp) cc_final: -0.0317 (mtp) REVERT: A 504 MET cc_start: 0.4204 (mmp) cc_final: 0.3825 (tpp) REVERT: A 585 ARG cc_start: 0.4456 (ttt180) cc_final: 0.3833 (tpp-160) REVERT: B 381 MET cc_start: -0.3162 (ttm) cc_final: -0.4132 (tpt) REVERT: D 446 GLU cc_start: 0.3147 (mm-30) cc_final: 0.2698 (mm-30) REVERT: D 634 MET cc_start: 0.7270 (tpp) cc_final: 0.6944 (tpp) outliers start: 6 outliers final: 3 residues processed: 282 average time/residue: 0.1676 time to fit residues: 75.5409 Evaluate side-chains 200 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 213 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 264 optimal weight: 30.0000 chunk 174 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 301 optimal weight: 0.8980 chunk 285 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.165167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.155403 restraints weight = 205507.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.154630 restraints weight = 148730.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.152668 restraints weight = 110922.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.151885 restraints weight = 136474.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.151455 restraints weight = 114126.889| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4604 r_free = 0.4604 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4604 r_free = 0.4604 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25118 Z= 0.122 Angle : 0.572 11.199 34039 Z= 0.299 Chirality : 0.041 0.148 3862 Planarity : 0.004 0.077 4325 Dihedral : 4.552 28.104 3363 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.05 (0.15), residues: 3094 helix: 0.96 (0.14), residues: 1396 sheet: -0.70 (0.24), residues: 426 loop : -0.83 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 787 TYR 0.028 0.002 TYR B 690 PHE 0.018 0.001 PHE C 705 TRP 0.022 0.001 TRP D 804 HIS 0.011 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00259 (25104) covalent geometry : angle 0.56980 (34011) SS BOND : bond 0.00348 ( 14) SS BOND : angle 1.69514 ( 28) hydrogen bonds : bond 0.04788 ( 1107) hydrogen bonds : angle 4.58376 ( 3218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.1237 (mt) cc_final: 0.0861 (mt) REVERT: A 295 MET cc_start: 0.2019 (mmt) cc_final: 0.0441 (mmp) REVERT: A 346 MET cc_start: 0.0575 (tpt) cc_final: -0.0024 (tpt) REVERT: A 504 MET cc_start: 0.4304 (mmp) cc_final: 0.3829 (tpp) REVERT: A 585 ARG cc_start: 0.4143 (ttt180) cc_final: 0.3674 (tpp-160) REVERT: B 83 MET cc_start: 0.1847 (ptt) cc_final: 0.1570 (ptt) REVERT: B 346 MET cc_start: 0.0944 (mtt) cc_final: 0.0265 (mtt) REVERT: B 381 MET cc_start: -0.3244 (ttm) cc_final: -0.4190 (tpp) REVERT: B 409 MET cc_start: -0.2099 (mmm) cc_final: -0.3035 (tpp) REVERT: B 557 LEU cc_start: 0.8225 (pt) cc_final: 0.7740 (mm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1656 time to fit residues: 67.7049 Evaluate side-chains 184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 218 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 297 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 237 optimal weight: 50.0000 chunk 275 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN C 179 GLN C 807 HIS D 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.165715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.156259 restraints weight = 196703.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.155821 restraints weight = 145445.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.154458 restraints weight = 105141.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.153957 restraints weight = 134857.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.153286 restraints weight = 121081.668| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4627 r_free = 0.4627 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4627 r_free = 0.4627 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25118 Z= 0.108 Angle : 0.549 9.741 34039 Z= 0.285 Chirality : 0.041 0.191 3862 Planarity : 0.004 0.071 4325 Dihedral : 4.330 27.578 3363 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.22 (0.15), residues: 3094 helix: 1.22 (0.14), residues: 1406 sheet: -0.50 (0.25), residues: 426 loop : -0.78 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.027 0.001 TYR B 690 PHE 0.022 0.001 PHE D 555 TRP 0.021 0.001 TRP B 709 HIS 0.006 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00224 (25104) covalent geometry : angle 0.54761 (34011) SS BOND : bond 0.00488 ( 14) SS BOND : angle 1.50826 ( 28) hydrogen bonds : bond 0.04224 ( 1107) hydrogen bonds : angle 4.35181 ( 3218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.1915 (mmt) cc_final: 0.0385 (mmp) REVERT: A 346 MET cc_start: 0.0425 (tpt) cc_final: -0.0189 (tpt) REVERT: A 504 MET cc_start: 0.4280 (mmp) cc_final: 0.4041 (tpp) REVERT: A 585 ARG cc_start: 0.4142 (ttt180) cc_final: 0.3722 (tpp-160) REVERT: B 83 MET cc_start: 0.1774 (ptt) cc_final: 0.1400 (ptt) REVERT: B 346 MET cc_start: 0.0460 (mtt) cc_final: -0.0157 (mtt) REVERT: B 409 MET cc_start: -0.2658 (mmm) cc_final: -0.3551 (tpp) REVERT: B 557 LEU cc_start: 0.8301 (pt) cc_final: 0.7809 (mm) REVERT: C 109 MET cc_start: 0.4583 (mmt) cc_final: 0.2085 (ptt) REVERT: C 677 MET cc_start: 0.7406 (mmm) cc_final: 0.6260 (tpt) REVERT: D 381 MET cc_start: -0.2009 (tmm) cc_final: -0.2716 (mtp) REVERT: D 504 MET cc_start: 0.4567 (mmt) cc_final: 0.4149 (mmt) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1565 time to fit residues: 60.2766 Evaluate side-chains 191 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 125 optimal weight: 0.4980 chunk 248 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 279 optimal weight: 2.9990 chunk 198 optimal weight: 0.0060 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 HIS C 807 HIS D 179 GLN D 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.152916 restraints weight = 192819.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.152517 restraints weight = 166822.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.151693 restraints weight = 128972.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.151435 restraints weight = 142139.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.151258 restraints weight = 103073.227| |-----------------------------------------------------------------------------| r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4600 r_free = 0.4600 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4600 r_free = 0.4600 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4566 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25118 Z= 0.135 Angle : 0.573 11.880 34039 Z= 0.299 Chirality : 0.042 0.275 3862 Planarity : 0.004 0.069 4325 Dihedral : 4.382 27.190 3363 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 1.44 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.19 (0.15), residues: 3094 helix: 1.17 (0.14), residues: 1405 sheet: -0.33 (0.25), residues: 435 loop : -0.84 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 161 TYR 0.025 0.002 TYR B 690 PHE 0.025 0.002 PHE C 705 TRP 0.022 0.001 TRP D 804 HIS 0.005 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00295 (25104) covalent geometry : angle 0.57208 (34011) SS BOND : bond 0.00400 ( 14) SS BOND : angle 1.39262 ( 28) hydrogen bonds : bond 0.04609 ( 1107) hydrogen bonds : angle 4.49644 ( 3218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.1719 (ptp) cc_final: 0.1513 (tpp) REVERT: A 295 MET cc_start: 0.2079 (mmt) cc_final: 0.0527 (mmp) REVERT: A 346 MET cc_start: 0.0283 (tpt) cc_final: -0.0213 (tpt) REVERT: A 381 MET cc_start: -0.0400 (mtp) cc_final: -0.1184 (mtp) REVERT: A 585 ARG cc_start: 0.4379 (ttt180) cc_final: 0.3832 (tpp-160) REVERT: B 83 MET cc_start: 0.1736 (ptt) cc_final: 0.1461 (ptt) REVERT: B 346 MET cc_start: -0.0163 (mtt) cc_final: -0.0600 (mtt) REVERT: B 409 MET cc_start: -0.2706 (mmm) cc_final: -0.3595 (tpp) REVERT: B 557 LEU cc_start: 0.8271 (pt) cc_final: 0.7767 (mm) REVERT: C 109 MET cc_start: 0.4778 (mmt) cc_final: 0.1935 (ptt) REVERT: C 212 MET cc_start: 0.3376 (ppp) cc_final: 0.2258 (ppp) REVERT: C 537 MET cc_start: 0.4993 (ttp) cc_final: 0.4587 (ttp) REVERT: C 663 ASN cc_start: 0.7394 (t0) cc_final: 0.6822 (p0) REVERT: C 677 MET cc_start: 0.7743 (mmm) cc_final: 0.6352 (tpt) REVERT: D 504 MET cc_start: 0.4806 (mmt) cc_final: 0.4371 (mmt) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1527 time to fit residues: 55.8174 Evaluate side-chains 183 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 178 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 chunk 186 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 494 HIS C 807 HIS D 389 ASN D 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.161738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.152449 restraints weight = 160975.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.151673 restraints weight = 134343.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.150456 restraints weight = 118826.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.150122 restraints weight = 127541.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.149803 restraints weight = 104339.341| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4580 r_free = 0.4580 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4580 r_free = 0.4580 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4636 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25118 Z= 0.153 Angle : 0.611 9.736 34039 Z= 0.319 Chirality : 0.043 0.226 3862 Planarity : 0.004 0.068 4325 Dihedral : 4.543 27.661 3363 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.00 (0.15), residues: 3094 helix: 0.98 (0.14), residues: 1416 sheet: -0.24 (0.25), residues: 432 loop : -1.00 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.026 0.002 TYR B 690 PHE 0.025 0.002 PHE C 705 TRP 0.028 0.002 TRP B 709 HIS 0.006 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00333 (25104) covalent geometry : angle 0.60934 (34011) SS BOND : bond 0.00332 ( 14) SS BOND : angle 1.63860 ( 28) hydrogen bonds : bond 0.04899 ( 1107) hydrogen bonds : angle 4.65702 ( 3218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.1314 (mt) cc_final: 0.0985 (mt) REVERT: A 167 MET cc_start: 0.2015 (ptp) cc_final: 0.1543 (tmm) REVERT: A 191 ASP cc_start: 0.3875 (m-30) cc_final: 0.3382 (t70) REVERT: A 295 MET cc_start: 0.1840 (mmt) cc_final: 0.0447 (mmp) REVERT: A 381 MET cc_start: -0.0660 (mtp) cc_final: -0.1488 (mtp) REVERT: A 585 ARG cc_start: 0.4531 (ttt180) cc_final: 0.3838 (tpp-160) REVERT: B 83 MET cc_start: 0.1709 (ptt) cc_final: 0.1381 (ptt) REVERT: B 346 MET cc_start: -0.0240 (mtt) cc_final: -0.0657 (mtt) REVERT: B 409 MET cc_start: -0.2103 (mmm) cc_final: -0.3244 (tpp) REVERT: C 109 MET cc_start: 0.4824 (mmt) cc_final: 0.1871 (ptt) REVERT: C 663 ASN cc_start: 0.7458 (t0) cc_final: 0.6960 (p0) REVERT: C 677 MET cc_start: 0.8059 (mmm) cc_final: 0.6825 (tpt) REVERT: D 504 MET cc_start: 0.5187 (mmt) cc_final: 0.4714 (mmt) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1545 time to fit residues: 56.3072 Evaluate side-chains 178 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 213 optimal weight: 0.0980 chunk 307 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 142 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 238 optimal weight: 50.0000 chunk 205 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 ASN C 807 HIS D 389 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.152908 restraints weight = 201523.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.152666 restraints weight = 167302.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.151406 restraints weight = 124909.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.150922 restraints weight = 135643.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.150190 restraints weight = 115183.002| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4588 r_free = 0.4588 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4588 r_free = 0.4588 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4611 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25118 Z= 0.116 Angle : 0.557 12.176 34039 Z= 0.288 Chirality : 0.041 0.206 3862 Planarity : 0.004 0.069 4325 Dihedral : 4.311 27.549 3363 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.19 (0.15), residues: 3094 helix: 1.24 (0.14), residues: 1411 sheet: -0.33 (0.26), residues: 433 loop : -0.95 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.029 0.001 TYR B 690 PHE 0.037 0.001 PHE B 691 TRP 0.029 0.001 TRP B 709 HIS 0.006 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00242 (25104) covalent geometry : angle 0.55507 (34011) SS BOND : bond 0.00205 ( 14) SS BOND : angle 1.55481 ( 28) hydrogen bonds : bond 0.04272 ( 1107) hydrogen bonds : angle 4.39118 ( 3218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.3768 (m-30) cc_final: 0.3349 (t70) REVERT: A 295 MET cc_start: 0.1765 (mmt) cc_final: 0.0399 (mmp) REVERT: A 381 MET cc_start: -0.0983 (mtp) cc_final: -0.1616 (mtp) REVERT: A 585 ARG cc_start: 0.4460 (ttt180) cc_final: 0.3807 (tpp-160) REVERT: B 83 MET cc_start: 0.1607 (ptt) cc_final: 0.1345 (ptt) REVERT: B 346 MET cc_start: -0.0365 (mtt) cc_final: -0.2662 (tmm) REVERT: B 409 MET cc_start: -0.2074 (mmm) cc_final: -0.3931 (ttm) REVERT: B 557 LEU cc_start: 0.8294 (pt) cc_final: 0.7918 (mm) REVERT: C 109 MET cc_start: 0.4565 (mmt) cc_final: 0.1906 (ptt) REVERT: C 212 MET cc_start: 0.3197 (ppp) cc_final: -0.0928 (mtt) REVERT: C 663 ASN cc_start: 0.7330 (t0) cc_final: 0.6817 (p0) REVERT: C 677 MET cc_start: 0.7674 (mmm) cc_final: 0.6315 (tpt) REVERT: D 167 MET cc_start: 0.6023 (tmm) cc_final: 0.5801 (tmm) REVERT: D 504 MET cc_start: 0.4669 (mmt) cc_final: 0.4249 (mmp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1538 time to fit residues: 59.1951 Evaluate side-chains 184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 144 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 191 optimal weight: 30.0000 chunk 164 optimal weight: 0.0270 chunk 241 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 overall best weight: 3.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN C 807 HIS D 389 ASN D 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.159666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.149475 restraints weight = 190753.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.149114 restraints weight = 173295.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.147978 restraints weight = 126635.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.147171 restraints weight = 142731.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.146557 restraints weight = 118088.424| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4798 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25118 Z= 0.209 Angle : 0.677 12.651 34039 Z= 0.358 Chirality : 0.045 0.245 3862 Planarity : 0.005 0.070 4325 Dihedral : 4.818 27.946 3363 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.24 (0.15), residues: 3094 helix: 0.78 (0.14), residues: 1398 sheet: -0.22 (0.25), residues: 432 loop : -1.15 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 692 TYR 0.028 0.002 TYR A 770 PHE 0.051 0.002 PHE B 691 TRP 0.031 0.002 TRP B 709 HIS 0.008 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00445 (25104) covalent geometry : angle 0.67546 (34011) SS BOND : bond 0.00279 ( 14) SS BOND : angle 1.79074 ( 28) hydrogen bonds : bond 0.05521 ( 1107) hydrogen bonds : angle 4.96029 ( 3218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.1420 (mt) cc_final: 0.1099 (mt) REVERT: A 191 ASP cc_start: 0.3878 (m-30) cc_final: 0.3223 (t70) REVERT: A 228 ILE cc_start: 0.4004 (mt) cc_final: 0.3664 (mt) REVERT: A 295 MET cc_start: 0.1808 (mmt) cc_final: 0.0408 (mmp) REVERT: A 381 MET cc_start: -0.1119 (mtp) cc_final: -0.1818 (mtp) REVERT: A 585 ARG cc_start: 0.4469 (ttt180) cc_final: 0.3847 (tpp-160) REVERT: B 83 MET cc_start: 0.1808 (ptt) cc_final: 0.1546 (ptt) REVERT: B 346 MET cc_start: -0.0242 (mtt) cc_final: -0.2621 (tmm) REVERT: B 409 MET cc_start: -0.1789 (mmm) cc_final: -0.3860 (ttm) REVERT: C 109 MET cc_start: 0.4732 (mmt) cc_final: 0.1887 (ptt) REVERT: C 212 MET cc_start: 0.3459 (ppp) cc_final: 0.2290 (ppp) REVERT: C 663 ASN cc_start: 0.7567 (t0) cc_final: 0.6859 (p0) REVERT: C 677 MET cc_start: 0.8141 (mmm) cc_final: 0.6803 (tpt) REVERT: D 167 MET cc_start: 0.6167 (tmm) cc_final: 0.5791 (tmm) REVERT: D 504 MET cc_start: 0.5150 (mmt) cc_final: 0.4714 (mmt) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1574 time to fit residues: 54.7661 Evaluate side-chains 171 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 226 optimal weight: 1.9990 chunk 186 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 245 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS D 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.160673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.150184 restraints weight = 200423.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.149759 restraints weight = 166179.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.148700 restraints weight = 118197.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.148510 restraints weight = 118791.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.147981 restraints weight = 96660.249| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4560 r_free = 0.4560 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4560 r_free = 0.4560 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25118 Z= 0.146 Angle : 0.616 10.606 34039 Z= 0.321 Chirality : 0.043 0.233 3862 Planarity : 0.004 0.073 4325 Dihedral : 4.640 27.524 3363 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.16 (0.15), residues: 3094 helix: 0.87 (0.14), residues: 1406 sheet: -0.27 (0.25), residues: 428 loop : -1.12 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.019 0.002 TYR A 770 PHE 0.047 0.002 PHE B 691 TRP 0.036 0.002 TRP B 709 HIS 0.012 0.001 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00316 (25104) covalent geometry : angle 0.61448 (34011) SS BOND : bond 0.00232 ( 14) SS BOND : angle 1.67351 ( 28) hydrogen bonds : bond 0.04872 ( 1107) hydrogen bonds : angle 4.73797 ( 3218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.1666 (mmt) cc_final: 0.0326 (mmp) REVERT: A 381 MET cc_start: -0.0877 (mtp) cc_final: -0.1635 (mtp) REVERT: A 585 ARG cc_start: 0.4712 (ttt180) cc_final: 0.3927 (tpp-160) REVERT: A 813 LEU cc_start: 0.6309 (mp) cc_final: 0.5665 (pp) REVERT: B 83 MET cc_start: 0.1705 (ptt) cc_final: 0.1430 (ptt) REVERT: B 346 MET cc_start: -0.0393 (mtt) cc_final: -0.2646 (tmm) REVERT: B 409 MET cc_start: -0.1989 (mmm) cc_final: -0.4113 (ttm) REVERT: C 212 MET cc_start: 0.3255 (ppp) cc_final: -0.1137 (mtt) REVERT: C 663 ASN cc_start: 0.7385 (t0) cc_final: 0.6802 (p0) REVERT: C 677 MET cc_start: 0.7938 (mmm) cc_final: 0.6488 (tpt) REVERT: D 167 MET cc_start: 0.5898 (tmm) cc_final: 0.5684 (tmm) REVERT: D 381 MET cc_start: -0.1751 (mmt) cc_final: -0.2487 (mtp) REVERT: D 504 MET cc_start: 0.4780 (mmt) cc_final: 0.4355 (mmp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1419 time to fit residues: 52.2015 Evaluate side-chains 174 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 72 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 184 optimal weight: 0.0170 chunk 261 optimal weight: 20.0000 chunk 288 optimal weight: 0.9990 chunk 8 optimal weight: 50.0000 chunk 222 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS D 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.161260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.150695 restraints weight = 202602.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.150427 restraints weight = 165441.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.149459 restraints weight = 125249.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.149041 restraints weight = 132487.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.148183 restraints weight = 110249.121| |-----------------------------------------------------------------------------| r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4564 r_free = 0.4564 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4564 r_free = 0.4564 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4684 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25118 Z= 0.123 Angle : 0.587 10.299 34039 Z= 0.305 Chirality : 0.042 0.231 3862 Planarity : 0.004 0.072 4325 Dihedral : 4.488 26.719 3363 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.03 (0.15), residues: 3094 helix: 1.03 (0.14), residues: 1414 sheet: -0.23 (0.25), residues: 432 loop : -1.12 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.019 0.002 TYR A 690 PHE 0.048 0.002 PHE B 691 TRP 0.037 0.001 TRP B 709 HIS 0.007 0.001 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00264 (25104) covalent geometry : angle 0.58573 (34011) SS BOND : bond 0.00223 ( 14) SS BOND : angle 1.54259 ( 28) hydrogen bonds : bond 0.04463 ( 1107) hydrogen bonds : angle 4.56282 ( 3218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.1648 (mmt) cc_final: 0.0303 (mmp) REVERT: A 381 MET cc_start: -0.1007 (mtp) cc_final: -0.1705 (mtp) REVERT: A 585 ARG cc_start: 0.4615 (ttt180) cc_final: 0.3783 (tpp-160) REVERT: A 813 LEU cc_start: 0.6204 (mp) cc_final: 0.5545 (pp) REVERT: B 83 MET cc_start: 0.1820 (ptt) cc_final: 0.1517 (ptt) REVERT: B 346 MET cc_start: -0.0321 (mtt) cc_final: -0.2613 (tmm) REVERT: B 365 MET cc_start: -0.5121 (tpt) cc_final: -0.5338 (tpt) REVERT: B 409 MET cc_start: -0.1971 (mmm) cc_final: -0.4091 (ttm) REVERT: B 557 LEU cc_start: 0.8278 (pt) cc_final: 0.7922 (mm) REVERT: C 109 MET cc_start: 0.4989 (mmt) cc_final: 0.1809 (ptt) REVERT: C 212 MET cc_start: 0.3077 (ppp) cc_final: -0.1154 (mtt) REVERT: C 663 ASN cc_start: 0.7386 (t0) cc_final: 0.6754 (p0) REVERT: C 677 MET cc_start: 0.7853 (mmm) cc_final: 0.6358 (tpt) REVERT: D 381 MET cc_start: -0.1725 (mmt) cc_final: -0.2774 (mtp) REVERT: D 504 MET cc_start: 0.4582 (mmt) cc_final: 0.4104 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1492 time to fit residues: 55.3555 Evaluate side-chains 174 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 51 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 195 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 253 optimal weight: 30.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN ** B 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.162612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.152210 restraints weight = 211814.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.152053 restraints weight = 175689.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.151015 restraints weight = 123901.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.150737 restraints weight = 131394.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.150105 restraints weight = 112101.085| |-----------------------------------------------------------------------------| r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4593 r_free = 0.4593 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4593 r_free = 0.4593 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.4593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4557 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25118 Z= 0.107 Angle : 0.562 9.843 34039 Z= 0.289 Chirality : 0.041 0.232 3862 Planarity : 0.004 0.072 4325 Dihedral : 4.284 26.900 3363 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.18 (0.15), residues: 3094 helix: 1.24 (0.14), residues: 1411 sheet: -0.02 (0.26), residues: 415 loop : -1.10 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 148 TYR 0.048 0.001 TYR B 690 PHE 0.064 0.001 PHE D 668 TRP 0.031 0.001 TRP B 709 HIS 0.006 0.000 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00225 (25104) covalent geometry : angle 0.56035 (34011) SS BOND : bond 0.00157 ( 14) SS BOND : angle 1.49789 ( 28) hydrogen bonds : bond 0.03956 ( 1107) hydrogen bonds : angle 4.34994 ( 3218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4288.91 seconds wall clock time: 75 minutes 1.96 seconds (4501.96 seconds total)