Starting phenix.real_space_refine on Thu May 22 15:51:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slq_40580/05_2025/8slq_40580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slq_40580/05_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_40580/05_2025/8slq_40580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slq_40580/05_2025/8slq_40580.map" model { file = "/net/cci-nas-00/data/ceres_data/8slq_40580/05_2025/8slq_40580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slq_40580/05_2025/8slq_40580.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 24, 'ASP:plan': 32, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 8, 'HIS:plan': 16, 'PHE:plan': 29, 'GLU:plan': 38, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 966 Restraints were copied for chains: C, B, D Time building chain proxies: 14.10, per 1000 atoms: 0.62 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: 5.85 Conformation dependent library (CDL) restraints added in 3.2 seconds 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 8 sheets defined 74.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 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: 8.80 Time building geometry restraints manager: 6.81 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.580 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 52.330 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (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 TRP 0.019 0.002 TRP C 773 HIS 0.004 0.001 HIS D 210 PHE 0.016 0.001 PHE C 289 TYR 0.010 0.001 TYR D 535 ARG 0.004 0.000 ARG D 722 Details of bonding type rmsd hydrogen bonds : bond 0.15015 ( 1760) hydrogen bonds : angle 6.21261 ( 5244) covalent geometry : bond 0.00302 (23312) covalent geometry : angle 0.64792 (32116) *********************** 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 : 0.589 Fit side-chains revert: symmetry clash REVERT: A 421 LEU cc_start: 0.9336 (mt) cc_final: 0.9133 (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: 0.1399 time to fit residues: 17.2895 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 : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 4.9990 chunk 272 optimal weight: 40.0000 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 282 optimal weight: 40.0000 chunk 109 optimal weight: 0.1980 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 GLN D 467 HIS D 737 ASN D 855 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059413 restraints weight = 30286.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061170 restraints weight = 18564.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062334 restraints weight = 13317.700| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23312 Z= 0.226 Angle : 0.598 6.564 32116 Z= 0.336 Chirality : 0.039 0.164 4028 Planarity : 0.005 0.087 4200 Dihedral : 4.430 18.392 3676 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3496 helix: 0.41 (0.10), residues: 2444 sheet: -0.02 (0.34), residues: 208 loop : -1.53 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 523 HIS 0.008 0.002 HIS D1004 PHE 0.017 0.002 PHE D 631 TYR 0.014 0.002 TYR D 535 ARG 0.004 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1760) hydrogen bonds : angle 4.85736 ( 5244) covalent geometry : bond 0.00420 (23312) covalent geometry : angle 0.59832 (32116) *********************** 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 78 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9161 (t60) cc_final: 0.8455 (t60) REVERT: D 993 LYS cc_start: 0.9763 (mttm) cc_final: 0.9388 (mttm) REVERT: D 1065 MET cc_start: 0.9375 (tpt) cc_final: 0.9173 (tpp) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.1305 time to fit residues: 14.6565 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 : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 134 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 271 optimal weight: 40.0000 chunk 234 optimal weight: 0.0870 chunk 265 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 overall best weight: 6.2166 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.085224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056594 restraints weight = 31804.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058300 restraints weight = 19509.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059476 restraints weight = 14061.320| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23312 Z= 0.296 Angle : 0.685 8.388 32116 Z= 0.381 Chirality : 0.041 0.183 4028 Planarity : 0.005 0.071 4200 Dihedral : 5.021 21.792 3676 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.57 % Allowed : 6.55 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3496 helix: 0.03 (0.10), residues: 2432 sheet: -0.57 (0.40), residues: 156 loop : -1.68 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 378 HIS 0.010 0.002 HIS D1004 PHE 0.024 0.003 PHE D 748 TYR 0.016 0.002 TYR B 587 ARG 0.004 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1760) hydrogen bonds : angle 5.19065 ( 5244) covalent geometry : bond 0.00544 (23312) covalent geometry : angle 0.68539 (32116) *********************** 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 65 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 740 MET cc_start: 0.8878 (ttp) cc_final: 0.8595 (tmm) REVERT: D 992 TRP cc_start: 0.9136 (t60) cc_final: 0.8597 (t60) REVERT: D 1065 MET cc_start: 0.9307 (tpt) cc_final: 0.9085 (tpp) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 0.1104 time to fit residues: 11.1595 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 : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 145 optimal weight: 0.9990 chunk 195 optimal weight: 0.0010 chunk 287 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 279 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 331 optimal weight: 10.0000 chunk 330 optimal weight: 0.3980 chunk 105 optimal weight: 0.0980 chunk 178 optimal weight: 6.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.089193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059919 restraints weight = 30010.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061813 restraints weight = 17827.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063133 restraints weight = 12583.444| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23312 Z= 0.117 Angle : 0.477 5.511 32116 Z= 0.266 Chirality : 0.037 0.145 4028 Planarity : 0.004 0.073 4200 Dihedral : 4.152 19.027 3676 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.57 % Allowed : 2.85 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3496 helix: 1.10 (0.10), residues: 2468 sheet: -0.59 (0.40), residues: 164 loop : -1.41 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 727 HIS 0.003 0.001 HIS A1004 PHE 0.014 0.001 PHE A 412 TYR 0.012 0.002 TYR D 750 ARG 0.002 0.000 ARG B 400 Details of bonding type rmsd hydrogen bonds : bond 0.02698 ( 1760) hydrogen bonds : angle 4.11262 ( 5244) covalent geometry : bond 0.00231 (23312) covalent geometry : angle 0.47739 (32116) *********************** 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 73 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: D 335 LYS cc_start: 0.9418 (tptt) cc_final: 0.9188 (ptpp) REVERT: D 557 MET cc_start: 0.8747 (mmp) cc_final: 0.8490 (tpp) REVERT: D 605 TRP cc_start: 0.8726 (m100) cc_final: 0.8344 (m100) REVERT: D 992 TRP cc_start: 0.9212 (t60) cc_final: 0.8756 (t60) REVERT: D 1065 MET cc_start: 0.9339 (tpt) cc_final: 0.9090 (tpp) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1151 time to fit residues: 12.5074 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 154 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 72 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.086062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057000 restraints weight = 31265.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.058777 restraints weight = 18825.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059978 restraints weight = 13465.832| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23312 Z= 0.253 Angle : 0.610 6.231 32116 Z= 0.345 Chirality : 0.039 0.158 4028 Planarity : 0.005 0.047 4200 Dihedral : 4.660 21.444 3676 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3496 helix: 0.77 (0.10), residues: 2436 sheet: -0.89 (0.40), residues: 164 loop : -1.51 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 523 HIS 0.006 0.002 HIS B1004 PHE 0.018 0.002 PHE C 631 TYR 0.016 0.002 TYR C 535 ARG 0.002 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 1760) hydrogen bonds : angle 4.76457 ( 5244) covalent geometry : bond 0.00464 (23312) covalent geometry : angle 0.60989 (32116) *********************** 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 64 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: D 992 TRP cc_start: 0.9184 (t60) cc_final: 0.8573 (t60) REVERT: D 1065 MET cc_start: 0.9354 (tpt) cc_final: 0.9120 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1131 time to fit residues: 11.0518 Evaluate side-chains 50 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 270 optimal weight: 50.0000 chunk 191 optimal weight: 50.0000 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 10 optimal weight: 40.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- 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 = 0.087443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063445 restraints weight = 36699.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062776 restraints weight = 25993.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062882 restraints weight = 19528.143| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23312 Z= 0.304 Angle : 0.675 8.204 32116 Z= 0.381 Chirality : 0.040 0.158 4028 Planarity : 0.005 0.069 4200 Dihedral : 5.203 24.557 3676 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3496 helix: 0.29 (0.10), residues: 2452 sheet: -1.52 (0.41), residues: 140 loop : -1.61 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 773 HIS 0.009 0.002 HIS A1004 PHE 0.021 0.003 PHE C 631 TYR 0.018 0.002 TYR B 587 ARG 0.004 0.001 ARG D 518 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1760) hydrogen bonds : angle 5.05060 ( 5244) covalent geometry : bond 0.00556 (23312) covalent geometry : angle 0.67532 (32116) *********************** 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 59 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: D 387 MET cc_start: 0.9209 (ppp) cc_final: 0.8954 (ppp) REVERT: D 748 PHE cc_start: 0.8921 (t80) cc_final: 0.8713 (t80) REVERT: D 750 TYR cc_start: 0.8266 (t80) cc_final: 0.8019 (t80) REVERT: D 992 TRP cc_start: 0.9142 (t60) cc_final: 0.8500 (t60) REVERT: D 1065 MET cc_start: 0.9293 (tpt) cc_final: 0.9088 (tpp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1202 time to fit residues: 10.8783 Evaluate side-chains 52 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 180 optimal weight: 50.0000 chunk 253 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 208 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.0080 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.088439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059316 restraints weight = 30499.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061131 restraints weight = 18425.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062351 restraints weight = 13134.080| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23312 Z= 0.120 Angle : 0.484 5.374 32116 Z= 0.272 Chirality : 0.037 0.145 4028 Planarity : 0.004 0.062 4200 Dihedral : 4.335 20.712 3676 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3496 helix: 1.19 (0.10), residues: 2452 sheet: -1.53 (0.36), residues: 164 loop : -1.49 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 727 HIS 0.003 0.001 HIS A1004 PHE 0.016 0.001 PHE C 412 TYR 0.011 0.002 TYR C 535 ARG 0.002 0.000 ARG C 400 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 1760) hydrogen bonds : angle 4.09840 ( 5244) covalent geometry : bond 0.00242 (23312) covalent geometry : angle 0.48387 (32116) *********************** 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 69 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: D 387 MET cc_start: 0.9250 (ppp) cc_final: 0.9016 (ppp) REVERT: D 419 GLN cc_start: 0.9558 (tt0) cc_final: 0.8712 (tp40) REVERT: D 748 PHE cc_start: 0.8995 (t80) cc_final: 0.8741 (t80) REVERT: D 992 TRP cc_start: 0.9116 (t60) cc_final: 0.8565 (t60) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1110 time to fit residues: 11.5377 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 : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 206 optimal weight: 0.0070 chunk 299 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 chunk 304 optimal weight: 0.0770 chunk 329 optimal weight: 0.7980 chunk 256 optimal weight: 30.0000 chunk 294 optimal weight: 30.0000 chunk 349 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061472 restraints weight = 30436.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063247 restraints weight = 18691.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064520 restraints weight = 13420.688| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23312 Z= 0.097 Angle : 0.455 5.049 32116 Z= 0.254 Chirality : 0.036 0.138 4028 Planarity : 0.004 0.067 4200 Dihedral : 3.906 18.462 3676 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3496 helix: 1.55 (0.11), residues: 2460 sheet: -0.88 (0.33), residues: 196 loop : -1.40 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 605 HIS 0.002 0.001 HIS B 210 PHE 0.026 0.001 PHE B1061 TYR 0.007 0.001 TYR A 997 ARG 0.002 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.02496 ( 1760) hydrogen bonds : angle 3.77300 ( 5244) covalent geometry : bond 0.00199 (23312) covalent geometry : angle 0.45495 (32116) *********************** 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 72 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: D 335 LYS cc_start: 0.9430 (tptt) cc_final: 0.9228 (mtmm) REVERT: D 387 MET cc_start: 0.9249 (ppp) cc_final: 0.8868 (ppp) REVERT: D 409 MET cc_start: 0.9172 (mmp) cc_final: 0.8959 (mmm) REVERT: D 419 GLN cc_start: 0.9577 (tt0) cc_final: 0.8732 (tp40) REVERT: D 748 PHE cc_start: 0.9020 (t80) cc_final: 0.8745 (t80) REVERT: D 992 TRP cc_start: 0.9163 (t60) cc_final: 0.8676 (t60) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1174 time to fit residues: 12.7512 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 152 optimal weight: 0.9980 chunk 349 optimal weight: 0.9980 chunk 95 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 35 optimal weight: 0.0980 chunk 198 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 69 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.090684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061788 restraints weight = 30017.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063614 restraints weight = 18567.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064863 restraints weight = 13322.042| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23312 Z= 0.094 Angle : 0.466 8.119 32116 Z= 0.254 Chirality : 0.036 0.136 4028 Planarity : 0.004 0.054 4200 Dihedral : 3.749 19.444 3676 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3496 helix: 1.74 (0.11), residues: 2448 sheet: -0.68 (0.35), residues: 172 loop : -1.17 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 523 HIS 0.003 0.001 HIS B 423 PHE 0.020 0.001 PHE C 432 TYR 0.007 0.001 TYR D 535 ARG 0.002 0.000 ARG C 400 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 1760) hydrogen bonds : angle 3.62912 ( 5244) covalent geometry : bond 0.00197 (23312) covalent geometry : angle 0.46600 (32116) *********************** 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 74 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: D 387 MET cc_start: 0.9233 (ppp) cc_final: 0.8820 (ppp) REVERT: D 409 MET cc_start: 0.9177 (mmp) cc_final: 0.8974 (mmm) REVERT: D 992 TRP cc_start: 0.9158 (t60) cc_final: 0.8679 (t60) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1142 time to fit residues: 12.8125 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 203 optimal weight: 0.0270 chunk 227 optimal weight: 6.9990 chunk 12 optimal weight: 50.0000 chunk 351 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 overall best weight: 2.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059443 restraints weight = 31278.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061281 restraints weight = 18921.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062590 restraints weight = 13463.579| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23312 Z= 0.147 Angle : 0.498 7.793 32116 Z= 0.279 Chirality : 0.037 0.139 4028 Planarity : 0.004 0.052 4200 Dihedral : 3.925 21.616 3676 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3496 helix: 1.63 (0.11), residues: 2440 sheet: -0.58 (0.36), residues: 172 loop : -1.00 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 605 HIS 0.003 0.001 HIS D1004 PHE 0.024 0.002 PHE C 432 TYR 0.011 0.001 TYR C 535 ARG 0.001 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 1760) hydrogen bonds : angle 3.90777 ( 5244) covalent geometry : bond 0.00292 (23312) covalent geometry : angle 0.49807 (32116) ********************** 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 69 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: D 387 MET cc_start: 0.9179 (ppp) cc_final: 0.8913 (ppp) REVERT: D 422 TYR cc_start: 0.8768 (m-80) cc_final: 0.7981 (m-80) REVERT: D 992 TRP cc_start: 0.9136 (t60) cc_final: 0.8574 (t60) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1159 time to fit residues: 12.2101 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 284 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 327 optimal weight: 0.2980 chunk 334 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 260 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.085522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057015 restraints weight = 32444.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058792 restraints weight = 19748.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059972 restraints weight = 14072.029| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23312 Z= 0.268 Angle : 0.623 7.287 32116 Z= 0.355 Chirality : 0.039 0.153 4028 Planarity : 0.005 0.048 4200 Dihedral : 4.652 25.220 3676 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3496 helix: 0.88 (0.11), residues: 2448 sheet: -0.84 (0.37), residues: 172 loop : -1.10 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 773 HIS 0.006 0.002 HIS A1004 PHE 0.038 0.003 PHE C 432 TYR 0.019 0.002 TYR C 535 ARG 0.003 0.001 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1760) hydrogen bonds : angle 4.60468 ( 5244) covalent geometry : bond 0.00501 (23312) covalent geometry : angle 0.62278 (32116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.95 seconds wall clock time: 67 minutes 43.62 seconds (4063.62 seconds total)