Starting phenix.real_space_refine on Sat Jul 4 19:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.map" model { file = "/net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slq_40580/07_2026/8slq_40580.cif" } resolution = 4.5 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= 0.002 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 68 5.16 5 C 14584 2.51 5 N 4072 2.21 5 O 4192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22916 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 5729 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 441} Link IDs: {'PTRANS': 35, 'TRANS': 870} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1703 Unresolved non-hydrogen angles: 2168 Unresolved non-hydrogen dihedrals: 1423 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLU:plan': 38, 'ASN:plan1': 12, 'PHE:plan': 29, 'ARG:plan': 38, 'TRP:plan': 8, 'HIS:plan': 16, 'ASP:plan': 32, 'GLN:plan1': 24, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 966 Restraints were copied for chains: D, B, C Time building chain proxies: 6.18, per 1000 atoms: 0.27 Number of scatterers: 22916 At special positions: 0 Unit cell: (153.44, 153.44, 148.96, 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 68 16.00 O 4192 8.00 N 4072 7.00 C 14584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 8 sheets defined 74.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 81 through 100 removed outlier: 3.971A pdb=" N VAL A 87 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.536A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 261 through 271 removed outlier: 4.087A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.705A pdb=" N ILE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.664A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.723A pdb=" N GLU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.770A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 542 through 557 removed outlier: 3.981A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.599A pdb=" N THR A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 removed outlier: 4.212A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 600 removed outlier: 3.865A pdb=" N ALA A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.610A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.608A pdb=" N TRP A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.557A pdb=" N ILE A 659 " --> pdb=" O CYS A 655 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR A 660 " --> pdb=" O PRO A 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 661' Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.725A pdb=" N ALA A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 754 Processing helix chain 'A' and resid 760 through 787 removed outlier: 4.193A pdb=" N TRP A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 3.987A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.649A pdb=" N THR A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 848 Processing helix chain 'A' and resid 849 through 855 removed outlier: 4.184A pdb=" N ALA A 853 " --> pdb=" O HIS A 850 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 869 removed outlier: 4.421A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.814A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.780A pdb=" N ILE A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 923 through 930 removed outlier: 3.878A pdb=" N GLU A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 removed outlier: 4.035A pdb=" N LEU A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 984 removed outlier: 3.740A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1005 Processing helix chain 'A' and resid 1010 through 1028 removed outlier: 3.555A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.972A pdb=" N VAL D 87 " --> pdb=" O TRP D 83 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.537A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 261 through 271 removed outlier: 4.088A pdb=" N VAL D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 295 through 311 removed outlier: 3.706A pdb=" N ILE D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.664A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 395 through 405 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.723A pdb=" N GLU D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 528 removed outlier: 3.769A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 542 through 557 removed outlier: 3.981A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 removed outlier: 3.599A pdb=" N THR D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 570 " --> pdb=" O VAL D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 589 removed outlier: 4.212A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 600 removed outlier: 3.865A pdb=" N ALA D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 618 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.611A pdb=" N PHE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.607A pdb=" N TRP D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 655 Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.556A pdb=" N ILE D 659 " --> pdb=" O CYS D 655 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 660 " --> pdb=" O PRO D 656 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 661' Processing helix chain 'D' and resid 717 through 729 removed outlier: 3.726A pdb=" N ALA D 729 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 754 Processing helix chain 'D' and resid 760 through 787 removed outlier: 4.193A pdb=" N TRP D 773 " --> pdb=" O THR D 769 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 804 removed outlier: 3.987A pdb=" N ASP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 826 removed outlier: 3.649A pdb=" N THR D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS D 823 " --> pdb=" O VAL D 819 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 848 Processing helix chain 'D' and resid 849 through 855 removed outlier: 4.185A pdb=" N ALA D 853 " --> pdb=" O HIS D 850 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 854 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 869 removed outlier: 4.422A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 895 removed outlier: 3.814A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 876 " --> pdb=" O VAL D 872 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D 877 " --> pdb=" O PHE D 873 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 879 " --> pdb=" O PHE D 875 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 918 removed outlier: 3.781A pdb=" N ILE D 904 " --> pdb=" O ARG D 900 " (cutoff:3.500A) Proline residue: D 912 - end of helix Processing helix chain 'D' and resid 923 through 930 removed outlier: 3.878A pdb=" N GLU D 927 " --> pdb=" O ASP D 923 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 928 " --> pdb=" O GLU D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 966 removed outlier: 4.036A pdb=" N LEU D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 984 removed outlier: 3.740A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1005 Processing helix chain 'D' and resid 1010 through 1028 removed outlier: 3.555A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1092 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 81 through 100 removed outlier: 3.971A pdb=" N VAL B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.537A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 261 through 271 removed outlier: 4.087A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.706A pdb=" N ILE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.664A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.723A pdb=" N GLU B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 528 removed outlier: 3.770A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.980A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.599A pdb=" N THR B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 570 " --> pdb=" O VAL B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 removed outlier: 4.213A pdb=" N LEU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 removed outlier: 3.866A pdb=" N ALA B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.609A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.608A pdb=" N TRP B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 655 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.556A pdb=" N ILE B 659 " --> pdb=" O CYS B 655 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR B 660 " --> pdb=" O PRO B 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 661' Processing helix chain 'B' and resid 717 through 729 removed outlier: 3.725A pdb=" N ALA B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 754 Processing helix chain 'B' and resid 760 through 787 removed outlier: 4.193A pdb=" N TRP B 773 " --> pdb=" O THR B 769 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 804 removed outlier: 3.988A pdb=" N ASP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 826 removed outlier: 3.649A pdb=" N THR B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS B 823 " --> pdb=" O VAL B 819 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 848 Processing helix chain 'B' and resid 849 through 855 removed outlier: 4.184A pdb=" N ALA B 853 " --> pdb=" O HIS B 850 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 869 removed outlier: 4.422A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 895 removed outlier: 3.813A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 879 " --> pdb=" O PHE B 875 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 918 removed outlier: 3.780A pdb=" N ILE B 904 " --> pdb=" O ARG B 900 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 923 through 930 removed outlier: 3.877A pdb=" N GLU B 927 " --> pdb=" O ASP B 923 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 966 removed outlier: 4.035A pdb=" N LEU B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 984 removed outlier: 3.740A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1005 Processing helix chain 'B' and resid 1010 through 1028 removed outlier: 3.554A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1092 Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 81 through 100 removed outlier: 3.971A pdb=" N VAL C 87 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.536A pdb=" N HIS C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 261 through 271 removed outlier: 4.088A pdb=" N VAL C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.705A pdb=" N ILE C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.664A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 443 removed outlier: 3.723A pdb=" N GLU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 515 through 528 removed outlier: 3.771A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 539 Processing helix chain 'C' and resid 542 through 557 removed outlier: 3.981A pdb=" N ALA C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.599A pdb=" N THR C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 589 removed outlier: 4.212A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 600 removed outlier: 3.866A pdb=" N ALA C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.610A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.607A pdb=" N TRP C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 655 Processing helix chain 'C' and resid 655 through 661 removed outlier: 3.557A pdb=" N ILE C 659 " --> pdb=" O CYS C 655 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR C 660 " --> pdb=" O PRO C 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 661' Processing helix chain 'C' and resid 717 through 729 removed outlier: 3.725A pdb=" N ALA C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 754 Processing helix chain 'C' and resid 760 through 787 removed outlier: 4.193A pdb=" N TRP C 773 " --> pdb=" O THR C 769 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 774 " --> pdb=" O LEU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 804 removed outlier: 3.987A pdb=" N ASP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 removed outlier: 3.649A pdb=" N THR C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS C 823 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG C 824 " --> pdb=" O GLY C 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 848 Processing helix chain 'C' and resid 849 through 855 removed outlier: 4.184A pdb=" N ALA C 853 " --> pdb=" O HIS C 850 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 854 " --> pdb=" O ILE C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 869 removed outlier: 4.421A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 895 removed outlier: 3.814A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE C 877 " --> pdb=" O PHE C 873 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 879 " --> pdb=" O PHE C 875 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 918 removed outlier: 3.781A pdb=" N ILE C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 923 through 930 removed outlier: 3.879A pdb=" N GLU C 927 " --> pdb=" O ASP C 923 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 928 " --> pdb=" O GLU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 966 removed outlier: 4.035A pdb=" N LEU C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 984 removed outlier: 3.739A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1005 Processing helix chain 'C' and resid 1010 through 1028 removed outlier: 3.555A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 8.276A pdb=" N ALA A 136 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE A 186 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 103 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET A 139 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 105 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N SER A 141 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 71 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 68 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A 231 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER A 70 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 255 Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 28 removed outlier: 8.277A pdb=" N ALA D 136 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE D 186 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 103 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET D 139 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR D 105 " --> pdb=" O MET D 139 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N SER D 141 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 71 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 68 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU D 231 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER D 70 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 28 removed outlier: 8.276A pdb=" N ALA B 136 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE B 186 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 105 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N SER B 141 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 71 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 68 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 231 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER B 70 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 253 through 255 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 28 removed outlier: 8.276A pdb=" N ALA C 136 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE C 186 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 103 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET C 139 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 105 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N SER C 141 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 71 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 253 through 255 1760 hydrogen bonds defined for protein. 5244 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: 4.52 Time building geometry restraints manager: 3.04 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: 7816 1.34 - 1.46: 3599 1.46 - 1.57: 11801 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 23312 Sorted by residual: bond pdb=" C ILE C 635 " pdb=" N TRP C 636 " ideal model delta sigma weight residual 1.335 1.421 -0.086 1.35e-02 5.49e+03 4.10e+01 bond pdb=" C ILE B 635 " pdb=" N TRP B 636 " ideal model delta sigma weight residual 1.335 1.421 -0.086 1.35e-02 5.49e+03 4.03e+01 bond pdb=" C ILE A 635 " pdb=" N TRP A 636 " ideal model delta sigma weight residual 1.335 1.420 -0.085 1.35e-02 5.49e+03 3.98e+01 bond pdb=" C ILE D 635 " pdb=" N TRP D 636 " ideal model delta sigma weight residual 1.335 1.420 -0.085 1.35e-02 5.49e+03 3.93e+01 bond pdb=" CA THR D 642 " pdb=" CB THR D 642 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.81e+00 ... (remaining 23307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 30717 1.42 - 2.83: 1136 2.83 - 4.25: 204 4.25 - 5.67: 39 5.67 - 7.08: 20 Bond angle restraints: 32116 Sorted by residual: angle pdb=" N TYR C 913 " pdb=" CA TYR C 913 " pdb=" C TYR C 913 " ideal model delta sigma weight residual 111.14 104.06 7.08 1.08e+00 8.57e-01 4.30e+01 angle pdb=" N TYR A 913 " pdb=" CA TYR A 913 " pdb=" C TYR A 913 " ideal model delta sigma weight residual 111.14 104.06 7.08 1.08e+00 8.57e-01 4.30e+01 angle pdb=" N TYR D 913 " pdb=" CA TYR D 913 " pdb=" C TYR D 913 " ideal model delta sigma weight residual 111.14 104.06 7.08 1.08e+00 8.57e-01 4.29e+01 angle pdb=" N TYR B 913 " pdb=" CA TYR B 913 " pdb=" C TYR B 913 " ideal model delta sigma weight residual 111.14 104.07 7.07 1.08e+00 8.57e-01 4.29e+01 angle pdb=" C VAL C 964 " pdb=" N THR C 965 " pdb=" CA THR C 965 " ideal model delta sigma weight residual 120.89 115.03 5.86 1.50e+00 4.44e-01 1.53e+01 ... (remaining 32111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 12604 15.07 - 30.14: 634 30.14 - 45.22: 182 45.22 - 60.29: 16 60.29 - 75.36: 8 Dihedral angle restraints: 13444 sinusoidal: 2888 harmonic: 10556 Sorted by residual: dihedral pdb=" CA PHE A 756 " pdb=" C PHE A 756 " pdb=" N ARG A 757 " pdb=" CA ARG A 757 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE C 756 " pdb=" C PHE C 756 " pdb=" N ARG C 757 " pdb=" CA ARG C 757 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE D 756 " pdb=" C PHE D 756 " pdb=" N ARG D 757 " pdb=" CA ARG D 757 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 13441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3594 0.062 - 0.124: 406 0.124 - 0.186: 24 0.186 - 0.248: 0 0.248 - 0.310: 4 Chirality restraints: 4028 Sorted by residual: chirality pdb=" CA THR C 642 " pdb=" N THR C 642 " pdb=" C THR C 642 " pdb=" CB THR C 642 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA THR A 642 " pdb=" N THR A 642 " pdb=" C THR A 642 " pdb=" CB THR A 642 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA THR B 642 " pdb=" N THR B 642 " pdb=" C THR B 642 " pdb=" CB THR B 642 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 4025 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 759 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO B 760 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 759 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 760 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 759 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 760 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 760 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 760 " 0.045 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 420 2.70 - 3.25: 25852 3.25 - 3.80: 36215 3.80 - 4.35: 40914 4.35 - 4.90: 64401 Nonbonded interactions: 167802 Sorted by model distance: nonbonded pdb=" O SER B 426 " pdb=" OG SER B 429 " model vdw 2.147 3.040 nonbonded pdb=" O SER C 426 " pdb=" OG SER C 429 " model vdw 2.147 3.040 nonbonded pdb=" O SER A 426 " pdb=" OG SER A 429 " model vdw 2.148 3.040 nonbonded pdb=" O SER D 426 " pdb=" OG SER D 429 " model vdw 2.148 3.040 nonbonded pdb=" O PHE D 746 " pdb=" OG SER D 749 " model vdw 2.207 3.040 ... (remaining 167797 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 23312 Z= 0.185 Angle : 0.648 7.085 32116 Z= 0.428 Chirality : 0.040 0.310 4028 Planarity : 0.005 0.081 4200 Dihedral : 10.868 75.361 6500 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 3496 helix: -0.81 (0.10), residues: 2420 sheet: -0.34 (0.36), residues: 184 loop : -2.10 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 722 TYR 0.010 0.001 TYR D 535 PHE 0.016 0.001 PHE C 289 TRP 0.019 0.002 TRP C 773 HIS 0.004 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.18 (23312) covalent geometry : angle 0.64792 / 0.43 (32116) hydrogen bonds : bond 0.15015 / 10.86 ( 1760) hydrogen bonds : angle 6.21261 / 4.63 ( 5244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 421 LEU cc_start: 0.9336 (mt) cc_final: 0.9134 (mt) REVERT: A 872 VAL cc_start: 0.9352 (p) cc_final: 0.8990 (m) REVERT: A 993 LYS cc_start: 0.9730 (mttm) cc_final: 0.9526 (mtmm) REVERT: A 1065 MET cc_start: 0.8920 (tpt) cc_final: 0.8643 (tpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0590 time to fit residues: 7.4328 Evaluate side-chains 67 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 0.0060 overall best weight: 2.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 737 ASN A 855 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061090 restraints weight = 30497.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062942 restraints weight = 18320.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064209 restraints weight = 12952.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065108 restraints weight = 10111.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065643 restraints weight = 8575.639| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23312 Z= 0.146 Angle : 0.519 6.474 32116 Z= 0.291 Chirality : 0.037 0.163 4028 Planarity : 0.005 0.091 4200 Dihedral : 4.097 16.758 3676 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.57 % Allowed : 3.70 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.14), residues: 3496 helix: 0.81 (0.10), residues: 2444 sheet: -0.05 (0.33), residues: 208 loop : -1.49 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.012 0.001 TYR D 530 PHE 0.012 0.001 PHE A 631 TRP 0.018 0.002 TRP A 523 HIS 0.007 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (23312) covalent geometry : angle 0.51852 / 0.29 (32116) hydrogen bonds : bond 0.03181 / 2.32 ( 1760) hydrogen bonds : angle 4.53097 / 3.42 ( 5244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 243 MET cc_start: 0.7795 (ttp) cc_final: 0.7143 (ptt) REVERT: D 992 TRP cc_start: 0.9184 (t60) cc_final: 0.8483 (t60) REVERT: D 993 LYS cc_start: 0.9724 (mttm) cc_final: 0.9330 (mttm) REVERT: D 1065 MET cc_start: 0.9349 (tpt) cc_final: 0.9098 (tpp) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.0613 time to fit residues: 7.2100 Evaluate side-chains 63 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.0970 chunk 193 optimal weight: 40.0000 chunk 331 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 225 GLN D 737 ASN D 855 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.087386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.058363 restraints weight = 31084.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060198 restraints weight = 18537.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061414 restraints weight = 13114.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062227 restraints weight = 10333.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062799 restraints weight = 8802.359| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23312 Z= 0.220 Angle : 0.577 6.461 32116 Z= 0.324 Chirality : 0.038 0.174 4028 Planarity : 0.005 0.069 4200 Dihedral : 4.311 18.549 3676 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3496 helix: 1.03 (0.10), residues: 2460 sheet: 0.16 (0.34), residues: 208 loop : -1.46 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 518 TYR 0.015 0.002 TYR C 535 PHE 0.018 0.002 PHE C 412 TRP 0.015 0.002 TRP D 727 HIS 0.007 0.002 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.22 (23312) covalent geometry : angle 0.57677 / 0.32 (32116) hydrogen bonds : bond 0.03294 / 2.39 ( 1760) hydrogen bonds : angle 4.64785 / 3.50 ( 5244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: B 387 MET cc_start: 0.9561 (ptm) cc_final: 0.9276 (ptm) REVERT: B 422 TYR cc_start: 0.9072 (m-80) cc_final: 0.8809 (m-80) REVERT: B 970 MET cc_start: 0.8807 (ttt) cc_final: 0.8577 (tpp) REVERT: B 992 TRP cc_start: 0.9113 (t60) cc_final: 0.8586 (t60) REVERT: B 993 LYS cc_start: 0.9778 (mttm) cc_final: 0.9330 (mttm) REVERT: B 1065 MET cc_start: 0.9317 (tpt) cc_final: 0.9041 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0478 time to fit residues: 5.5394 Evaluate side-chains 56 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 7 optimal weight: 50.0000 chunk 137 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 254 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 180 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN B 855 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056552 restraints weight = 31655.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058288 restraints weight = 19129.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059466 restraints weight = 13645.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060259 restraints weight = 10829.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060818 restraints weight = 9251.802| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23312 Z= 0.298 Angle : 0.673 8.471 32116 Z= 0.377 Chirality : 0.040 0.158 4028 Planarity : 0.005 0.083 4200 Dihedral : 4.838 20.522 3676 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.57 % Allowed : 6.27 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3496 helix: 0.82 (0.10), residues: 2464 sheet: -0.45 (0.39), residues: 156 loop : -1.42 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 417 TYR 0.017 0.003 TYR B 535 PHE 0.020 0.002 PHE B 631 TRP 0.016 0.002 TRP C 523 HIS 0.011 0.003 HIS D1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.30 (23312) covalent geometry : angle 0.67316 / 0.38 (32116) hydrogen bonds : bond 0.03757 / 2.73 ( 1760) hydrogen bonds : angle 5.00627 / 3.76 ( 5244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: D 740 MET cc_start: 0.8735 (ttp) cc_final: 0.8522 (tmm) REVERT: D 809 CYS cc_start: 0.9318 (m) cc_final: 0.9117 (m) REVERT: D 992 TRP cc_start: 0.9164 (t60) cc_final: 0.8626 (t60) REVERT: D 1065 MET cc_start: 0.9323 (tpt) cc_final: 0.9105 (tpp) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 0.0549 time to fit residues: 5.4795 Evaluate side-chains 55 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 59 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 289 optimal weight: 0.3980 chunk 321 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 180 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 855 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060815 restraints weight = 30280.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062712 restraints weight = 17799.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064013 restraints weight = 12456.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064883 restraints weight = 9748.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065499 restraints weight = 8218.600| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23312 Z= 0.102 Angle : 0.484 7.579 32116 Z= 0.266 Chirality : 0.037 0.147 4028 Planarity : 0.004 0.055 4200 Dihedral : 4.055 17.386 3676 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.14), residues: 3496 helix: 1.81 (0.11), residues: 2476 sheet: -0.31 (0.33), residues: 196 loop : -1.28 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 400 TYR 0.011 0.001 TYR D 660 PHE 0.014 0.001 PHE A 412 TRP 0.022 0.002 TRP B 253 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (23312) covalent geometry : angle 0.48430 / 0.27 (32116) hydrogen bonds : bond 0.02610 / 1.90 ( 1760) hydrogen bonds : angle 3.92894 / 2.98 ( 5244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 LYS cc_start: 0.9430 (tptt) cc_final: 0.9210 (ptpp) REVERT: D 387 MET cc_start: 0.9428 (ptm) cc_final: 0.9162 (ppp) REVERT: D 809 CYS cc_start: 0.9355 (m) cc_final: 0.9151 (m) REVERT: D 992 TRP cc_start: 0.9177 (t60) cc_final: 0.8693 (t60) REVERT: D 1065 MET cc_start: 0.9307 (tpt) cc_final: 0.9060 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0445 time to fit residues: 5.0676 Evaluate side-chains 58 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 273 optimal weight: 40.0000 chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 264 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.086460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057686 restraints weight = 32082.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059440 restraints weight = 19162.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060627 restraints weight = 13644.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061465 restraints weight = 10789.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061960 restraints weight = 9171.149| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23312 Z= 0.229 Angle : 0.578 5.858 32116 Z= 0.327 Chirality : 0.038 0.148 4028 Planarity : 0.005 0.065 4200 Dihedral : 4.390 19.353 3676 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.15), residues: 3496 helix: 1.62 (0.11), residues: 2492 sheet: -0.27 (0.34), residues: 196 loop : -1.40 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 242 TYR 0.015 0.002 TYR C 535 PHE 0.017 0.002 PHE C 631 TRP 0.016 0.002 TRP D 727 HIS 0.005 0.002 HIS D1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.23 (23312) covalent geometry : angle 0.57785 / 0.33 (32116) hydrogen bonds : bond 0.03171 / 2.30 ( 1760) hydrogen bonds : angle 4.49473 / 3.38 ( 5244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: D 809 CYS cc_start: 0.9355 (m) cc_final: 0.9146 (m) REVERT: D 992 TRP cc_start: 0.9161 (t60) cc_final: 0.8546 (t60) REVERT: D 993 LYS cc_start: 0.9748 (mttm) cc_final: 0.9465 (mttm) REVERT: D 1065 MET cc_start: 0.9282 (tpt) cc_final: 0.9037 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0499 time to fit residues: 4.8668 Evaluate side-chains 54 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 288 optimal weight: 0.0470 chunk 102 optimal weight: 30.0000 chunk 339 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 306 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 overall best weight: 2.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059260 restraints weight = 30977.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061125 restraints weight = 18316.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062367 restraints weight = 12863.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063272 restraints weight = 10111.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063866 restraints weight = 8520.077| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23312 Z= 0.135 Angle : 0.484 5.343 32116 Z= 0.272 Chirality : 0.037 0.147 4028 Planarity : 0.004 0.062 4200 Dihedral : 4.077 17.830 3676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.15), residues: 3496 helix: 1.97 (0.11), residues: 2472 sheet: -0.20 (0.35), residues: 196 loop : -1.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 400 TYR 0.011 0.002 TYR B 535 PHE 0.017 0.002 PHE A 744 TRP 0.019 0.002 TRP D 727 HIS 0.003 0.001 HIS B1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (23312) covalent geometry : angle 0.48440 / 0.27 (32116) hydrogen bonds : bond 0.02567 / 1.87 ( 1760) hydrogen bonds : angle 4.00656 / 3.02 ( 5244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 605 TRP cc_start: 0.8687 (m100) cc_final: 0.8215 (m100) REVERT: D 809 CYS cc_start: 0.9342 (m) cc_final: 0.9138 (m) REVERT: D 992 TRP cc_start: 0.9133 (t60) cc_final: 0.8562 (t60) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0510 time to fit residues: 5.6016 Evaluate side-chains 57 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 39 optimal weight: 0.0070 chunk 166 optimal weight: 50.0000 chunk 20 optimal weight: 0.4980 chunk 322 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 227 optimal weight: 0.0040 chunk 294 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 286 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.091095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061520 restraints weight = 29765.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063428 restraints weight = 17736.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064746 restraints weight = 12505.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065628 restraints weight = 9792.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066249 restraints weight = 8268.357| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23312 Z= 0.093 Angle : 0.454 5.076 32116 Z= 0.251 Chirality : 0.036 0.136 4028 Planarity : 0.004 0.065 4200 Dihedral : 3.637 17.207 3676 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.14), residues: 3496 helix: 2.37 (0.11), residues: 2452 sheet: 0.07 (0.36), residues: 196 loop : -1.04 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.007 0.001 TYR A 535 PHE 0.018 0.001 PHE B 744 TRP 0.022 0.002 TRP D 727 HIS 0.004 0.001 HIS C 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (23312) covalent geometry : angle 0.45444 / 0.25 (32116) hydrogen bonds : bond 0.02219 / 1.62 ( 1760) hydrogen bonds : angle 3.56839 / 2.70 ( 5244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: D 809 CYS cc_start: 0.9322 (m) cc_final: 0.9100 (m) REVERT: D 992 TRP cc_start: 0.9171 (t60) cc_final: 0.8656 (t60) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0494 time to fit residues: 6.2247 Evaluate side-chains 59 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 355 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 348 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 358 optimal weight: 8.9990 chunk 240 optimal weight: 0.2980 chunk 6 optimal weight: 30.0000 chunk 266 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.089048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060375 restraints weight = 30444.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062333 restraints weight = 17689.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063646 restraints weight = 12319.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064516 restraints weight = 9621.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065088 restraints weight = 8131.592| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23312 Z= 0.144 Angle : 0.505 8.040 32116 Z= 0.280 Chirality : 0.037 0.143 4028 Planarity : 0.004 0.052 4200 Dihedral : 3.754 16.297 3676 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.15), residues: 3496 helix: 2.24 (0.11), residues: 2460 sheet: -0.01 (0.35), residues: 196 loop : -0.98 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 363 TYR 0.011 0.001 TYR C 535 PHE 0.026 0.002 PHE D 744 TRP 0.046 0.002 TRP D 605 HIS 0.004 0.001 HIS C 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (23312) covalent geometry : angle 0.50478 / 0.28 (32116) hydrogen bonds : bond 0.02666 / 1.96 ( 1760) hydrogen bonds : angle 3.92911 / 2.96 ( 5244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 335 LYS cc_start: 0.9276 (mtmm) cc_final: 0.8982 (ptpt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0482 time to fit residues: 5.5552 Evaluate side-chains 54 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 281 optimal weight: 50.0000 chunk 211 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.091815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068513 restraints weight = 36443.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066880 restraints weight = 23940.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067193 restraints weight = 25251.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067169 restraints weight = 22458.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067487 restraints weight = 18694.939| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23312 Z= 0.159 Angle : 0.523 7.661 32116 Z= 0.292 Chirality : 0.037 0.146 4028 Planarity : 0.004 0.055 4200 Dihedral : 3.949 18.083 3676 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.15), residues: 3496 helix: 2.11 (0.11), residues: 2444 sheet: 0.05 (0.38), residues: 172 loop : -0.96 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.013 0.002 TYR D 535 PHE 0.030 0.002 PHE C1061 TRP 0.037 0.002 TRP D 605 HIS 0.003 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (23312) covalent geometry : angle 0.52271 / 0.29 (32116) hydrogen bonds : bond 0.02863 / 2.09 ( 1760) hydrogen bonds : angle 4.03758 / 3.04 ( 5244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9111 (t60) cc_final: 0.8606 (t60) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0555 time to fit residues: 5.8359 Evaluate side-chains 55 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 147 optimal weight: 0.8980 chunk 337 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 295 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 102 optimal weight: 50.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.085134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056895 restraints weight = 31902.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058665 restraints weight = 19156.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059871 restraints weight = 13671.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060603 restraints weight = 10811.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061181 restraints weight = 9255.889| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23312 Z= 0.283 Angle : 0.669 7.518 32116 Z= 0.376 Chirality : 0.040 0.155 4028 Planarity : 0.005 0.047 4200 Dihedral : 4.720 22.952 3676 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.14), residues: 3496 helix: 1.39 (0.11), residues: 2468 sheet: -0.56 (0.37), residues: 172 loop : -1.11 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.022 0.003 TYR C 535 PHE 0.028 0.003 PHE C 476 TRP 0.033 0.004 TRP D 605 HIS 0.006 0.002 HIS C1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.28 (23312) covalent geometry : angle 0.66943 / 0.38 (32116) hydrogen bonds : bond 0.03700 / 2.71 ( 1760) hydrogen bonds : angle 4.78177 / 3.58 ( 5244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.85 seconds wall clock time: 37 minutes 55.01 seconds (2275.01 seconds total)