Starting phenix.real_space_refine on Sun Aug 24 21:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slq_40580/08_2025/8slq_40580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slq_40580/08_2025/8slq_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_40580/08_2025/8slq_40580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slq_40580/08_2025/8slq_40580.map" model { file = "/net/cci-nas-00/data/ceres_data/8slq_40580/08_2025/8slq_40580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slq_40580/08_2025/8slq_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-2.0-5787/lib/python3.9/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: 4.58, per 1000 atoms: 0.20 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: 1.51 Conformation dependent library (CDL) restraints added in 767.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.98 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: 3.27 Time building geometry restraints manager: 2.06 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: 0.07 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.320 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 aren 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 covalent geometry : bond 0.00302 (23312) covalent geometry : angle 0.64792 (32116) hydrogen bonds : bond 0.15015 ( 1760) hydrogen bonds : angle 6.21261 ( 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 : 0.144 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: 0.0488 time to fit residues: 6.0918 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 : 0.191 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3742 r_free = 0.3742 target = 0.090520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061092 restraints weight = 30491.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062942 restraints weight = 18350.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064203 restraints weight = 12955.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065079 restraints weight = 10191.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065623 restraints weight = 8622.626| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2034 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 : 3.99 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 covalent geometry : bond 0.00285 (23312) covalent geometry : angle 0.51852 (32116) hydrogen bonds : bond 0.03181 ( 1760) hydrogen bonds : angle 4.53097 ( 5244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 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 : 0.187 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: 0.9183 (t60) cc_final: 0.8482 (t60) REVERT: D 993 LYS cc_start: 0.9724 (mttm) cc_final: 0.9329 (mttm) REVERT: D 1065 MET cc_start: 0.9348 (tpt) cc_final: 0.9098 (tpp) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.0515 time to fit residues: 6.0386 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 : 0.178 ------------------------------------------------------------------------------- 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: 0.3980 chunk 177 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 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: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.088804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059353 restraints weight = 30235.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061188 restraints weight = 18099.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062421 restraints weight = 12894.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063321 restraints weight = 10153.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063840 restraints weight = 8601.215| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23312 Z= 0.163 Angle : 0.504 5.114 32116 Z= 0.284 Chirality : 0.037 0.140 4028 Planarity : 0.004 0.069 4200 Dihedral : 4.001 18.788 3676 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.14), residues: 3496 helix: 1.09 (0.10), residues: 2468 sheet: 0.07 (0.33), residues: 208 loop : -1.45 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 242 TYR 0.012 0.002 TYR C 535 PHE 0.014 0.002 PHE B 631 TRP 0.016 0.002 TRP D 727 HIS 0.006 0.001 HIS A1004 Details of bonding type rmsd covalent geometry : bond 0.00310 (23312) covalent geometry : angle 0.50407 (32116) hydrogen bonds : bond 0.02877 ( 1760) hydrogen bonds : angle 4.29170 ( 5244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 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 : 0.218 Fit side-chains revert: symmetry clash REVERT: D 605 TRP cc_start: 0.8894 (m100) cc_final: 0.8308 (m100) REVERT: D 970 MET cc_start: 0.8758 (ttt) cc_final: 0.8536 (tpp) REVERT: D 992 TRP cc_start: 0.9204 (t60) cc_final: 0.8631 (t60) REVERT: D 993 LYS cc_start: 0.9759 (mttm) cc_final: 0.9413 (mttm) REVERT: D 1065 MET cc_start: 0.9352 (tpt) cc_final: 0.9116 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0411 time to fit residues: 4.6545 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 : 0.123 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 0.0020 chunk 183 optimal weight: 30.0000 chunk 254 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 chunk 180 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 overall best weight: 3.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.087389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058139 restraints weight = 30434.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059910 restraints weight = 18559.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061154 restraints weight = 13313.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061956 restraints weight = 10545.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062573 restraints weight = 9021.809| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23312 Z= 0.200 Angle : 0.551 5.503 32116 Z= 0.307 Chirality : 0.038 0.145 4028 Planarity : 0.005 0.072 4200 Dihedral : 4.245 18.695 3676 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.57 % Allowed : 5.70 % Favored : 93.73 % 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 aren not related in a simple way. whole: 0.56 (0.14), residues: 3496 helix: 1.07 (0.10), residues: 2472 sheet: -0.66 (0.37), residues: 164 loop : -1.35 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 242 TYR 0.014 0.002 TYR C 535 PHE 0.016 0.002 PHE C 631 TRP 0.016 0.002 TRP D 727 HIS 0.010 0.002 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00373 (23312) covalent geometry : angle 0.55078 (32116) hydrogen bonds : bond 0.02999 ( 1760) hydrogen bonds : angle 4.36692 ( 5244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 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: 2 poor density : 68 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: D 740 MET cc_start: 0.8811 (ttp) cc_final: 0.8575 (tmm) REVERT: D 970 MET cc_start: 0.8768 (ttt) cc_final: 0.8530 (tpp) REVERT: D 992 TRP cc_start: 0.9188 (t60) cc_final: 0.8639 (t60) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.0442 time to fit residues: 4.6693 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 : 0.204 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 180 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.086484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057453 restraints weight = 32236.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059240 restraints weight = 19211.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060478 restraints weight = 13651.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061292 restraints weight = 10772.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061870 restraints weight = 9171.686| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23312 Z= 0.242 Angle : 0.592 6.742 32116 Z= 0.332 Chirality : 0.038 0.143 4028 Planarity : 0.005 0.055 4200 Dihedral : 4.457 19.669 3676 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3496 helix: 0.82 (0.10), residues: 2484 sheet: -1.13 (0.36), residues: 164 loop : -1.44 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 245 TYR 0.015 0.002 TYR A 535 PHE 0.018 0.002 PHE C 631 TRP 0.026 0.002 TRP B 253 HIS 0.005 0.002 HIS B1004 Details of bonding type rmsd covalent geometry : bond 0.00446 (23312) covalent geometry : angle 0.59151 (32116) hydrogen bonds : bond 0.03319 ( 1760) hydrogen bonds : angle 4.63191 ( 5244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9180 (t60) cc_final: 0.8541 (t60) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0448 time to fit residues: 4.6202 Evaluate side-chains 51 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 9.9990 chunk 82 optimal weight: 4.9990 chunk 273 optimal weight: 0.0270 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059267 restraints weight = 31287.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061044 restraints weight = 19120.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062260 restraints weight = 13717.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063103 restraints weight = 10891.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063620 restraints weight = 9263.727| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23312 Z= 0.141 Angle : 0.489 5.935 32116 Z= 0.275 Chirality : 0.037 0.146 4028 Planarity : 0.004 0.055 4200 Dihedral : 4.054 16.592 3676 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 aren not related in a simple way. whole: 0.99 (0.14), residues: 3496 helix: 1.46 (0.11), residues: 2472 sheet: -0.77 (0.33), residues: 196 loop : -1.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 722 TYR 0.015 0.002 TYR B 660 PHE 0.016 0.002 PHE B 412 TRP 0.019 0.002 TRP C 727 HIS 0.004 0.001 HIS B1004 Details of bonding type rmsd covalent geometry : bond 0.00274 (23312) covalent geometry : angle 0.48850 (32116) hydrogen bonds : bond 0.02637 ( 1760) hydrogen bonds : angle 4.05640 ( 5244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 387 MET cc_start: 0.9416 (ptm) cc_final: 0.9034 (ppp) REVERT: D 992 TRP cc_start: 0.9144 (t60) cc_final: 0.8526 (t60) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0412 time to fit residues: 4.1357 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 : 0.162 ------------------------------------------------------------------------------- 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: 7.9990 chunk 102 optimal weight: 40.0000 chunk 339 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 187 optimal weight: 50.0000 chunk 306 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.088655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064566 restraints weight = 37667.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063607 restraints weight = 26195.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063811 restraints weight = 20183.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064102 restraints weight = 19655.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064182 restraints weight = 17225.015| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23312 Z= 0.262 Angle : 0.612 6.499 32116 Z= 0.347 Chirality : 0.039 0.156 4028 Planarity : 0.005 0.070 4200 Dihedral : 4.651 20.709 3676 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3496 helix: 0.93 (0.11), residues: 2456 sheet: -1.52 (0.39), residues: 140 loop : -1.46 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.017 0.002 TYR B 535 PHE 0.034 0.002 PHE C 744 TRP 0.022 0.003 TRP A 773 HIS 0.006 0.002 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00484 (23312) covalent geometry : angle 0.61191 (32116) hydrogen bonds : bond 0.03495 ( 1760) hydrogen bonds : angle 4.71117 ( 5244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 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: 0 poor density : 66 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: D 387 MET cc_start: 0.9354 (ptm) cc_final: 0.8983 (ppp) REVERT: D 992 TRP cc_start: 0.9113 (t60) cc_final: 0.8466 (t60) REVERT: D 993 LYS cc_start: 0.9773 (mttm) cc_final: 0.9448 (mttm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0512 time to fit residues: 5.0417 Evaluate side-chains 53 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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: 3.9990 chunk 166 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 322 optimal weight: 0.0970 chunk 146 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 294 optimal weight: 30.0000 chunk 105 optimal weight: 0.0470 chunk 286 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 overall best weight: 3.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059010 restraints weight = 31378.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060837 restraints weight = 18724.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062083 restraints weight = 13244.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062913 restraints weight = 10380.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063539 restraints weight = 8781.211| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23312 Z= 0.155 Angle : 0.492 5.115 32116 Z= 0.278 Chirality : 0.037 0.146 4028 Planarity : 0.004 0.065 4200 Dihedral : 4.187 18.683 3676 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3496 helix: 1.47 (0.11), residues: 2452 sheet: -1.61 (0.37), residues: 140 loop : -1.34 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 518 TYR 0.011 0.001 TYR C 535 PHE 0.018 0.002 PHE D 744 TRP 0.019 0.002 TRP D 727 HIS 0.005 0.001 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00295 (23312) covalent geometry : angle 0.49223 (32116) hydrogen bonds : bond 0.02707 ( 1760) hydrogen bonds : angle 4.11895 ( 5244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 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: 0 poor density : 66 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9159 (t60) cc_final: 0.8524 (t60) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0437 time to fit residues: 4.4402 Evaluate side-chains 53 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 0.4980 chunk 179 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 15 optimal weight: 0.0010 chunk 358 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 266 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 overall best weight: 3.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058356 restraints weight = 30855.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060104 restraints weight = 18820.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061319 restraints weight = 13438.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062156 restraints weight = 10592.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062736 restraints weight = 8968.152| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23312 Z= 0.189 Angle : 0.538 7.944 32116 Z= 0.304 Chirality : 0.038 0.146 4028 Planarity : 0.004 0.052 4200 Dihedral : 4.298 20.160 3676 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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 aren not related in a simple way. whole: 0.82 (0.14), residues: 3496 helix: 1.37 (0.11), residues: 2448 sheet: -1.63 (0.38), residues: 140 loop : -1.32 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 518 TYR 0.014 0.002 TYR D 535 PHE 0.028 0.002 PHE C 412 TRP 0.018 0.002 TRP B 727 HIS 0.005 0.002 HIS B1004 Details of bonding type rmsd covalent geometry : bond 0.00359 (23312) covalent geometry : angle 0.53751 (32116) hydrogen bonds : bond 0.03032 ( 1760) hydrogen bonds : angle 4.26526 ( 5244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9151 (t60) cc_final: 0.8544 (t60) REVERT: D 993 LYS cc_start: 0.9728 (mttm) cc_final: 0.9390 (mttm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0497 time to fit residues: 5.0986 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 : 0.132 ------------------------------------------------------------------------------- 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: 40.0000 chunk 211 optimal weight: 0.7980 chunk 309 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 340 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 359 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.086105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057484 restraints weight = 32654.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059266 restraints weight = 19725.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060440 restraints weight = 14070.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061304 restraints weight = 11114.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061873 restraints weight = 9429.730| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23312 Z= 0.234 Angle : 0.584 7.588 32116 Z= 0.333 Chirality : 0.038 0.153 4028 Planarity : 0.005 0.047 4200 Dihedral : 4.573 21.574 3676 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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 aren not related in a simple way. whole: 0.50 (0.14), residues: 3496 helix: 1.10 (0.11), residues: 2444 sheet: -1.76 (0.37), residues: 140 loop : -1.31 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 518 TYR 0.016 0.002 TYR D 535 PHE 0.020 0.002 PHE D 744 TRP 0.020 0.002 TRP D 773 HIS 0.006 0.002 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00438 (23312) covalent geometry : angle 0.58445 (32116) hydrogen bonds : bond 0.03387 ( 1760) hydrogen bonds : angle 4.54989 ( 5244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: D 409 MET cc_start: 0.9091 (mmp) cc_final: 0.8772 (mmm) REVERT: D 992 TRP cc_start: 0.9146 (t60) cc_final: 0.8572 (t60) REVERT: D 993 LYS cc_start: 0.9738 (mttm) cc_final: 0.9399 (mttm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0500 time to fit residues: 4.7458 Evaluate side-chains 53 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 9.9990 chunk 337 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 295 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 102 optimal weight: 50.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056876 restraints weight = 32626.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058476 restraints weight = 20614.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059574 restraints weight = 15048.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060318 restraints weight = 12100.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060824 restraints weight = 10407.050| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23312 Z= 0.296 Angle : 0.650 7.054 32116 Z= 0.370 Chirality : 0.039 0.155 4028 Planarity : 0.005 0.050 4200 Dihedral : 4.901 22.284 3676 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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 aren not related in a simple way. whole: -0.03 (0.14), residues: 3496 helix: 0.64 (0.10), residues: 2448 sheet: -1.89 (0.36), residues: 140 loop : -1.33 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 518 TYR 0.018 0.002 TYR B 587 PHE 0.051 0.003 PHE D 432 TRP 0.028 0.003 TRP C 773 HIS 0.008 0.002 HIS C1004 Details of bonding type rmsd covalent geometry : bond 0.00547 (23312) covalent geometry : angle 0.65049 (32116) hydrogen bonds : bond 0.03707 ( 1760) hydrogen bonds : angle 4.85295 ( 5244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.29 seconds wall clock time: 29 minutes 44.35 seconds (1784.35 seconds total)