Starting phenix.real_space_refine on Fri Aug 7 10:54:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sli_40578/08_2026/8sli_40578.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 40 5.16 5 C 13156 2.51 5 N 3876 2.21 5 O 3916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20996 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 5247 Classifications: {'peptide': 894} Incomplete info: {'truncation_to_alanine': 553} Link IDs: {'PTRANS': 34, 'TRANS': 859} Chain breaks: 17 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 2109 Unresolved non-hydrogen angles: 2702 Unresolved non-hydrogen dihedrals: 1753 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLU:plan': 48, 'ASN:plan1': 13, 'PHE:plan': 34, 'ARG:plan': 48, 'TRP:plan': 12, 'HIS:plan': 13, 'ASP:plan': 36, 'GLN:plan1': 24, 'TYR:plan': 16} Unresolved non-hydrogen planarities: 1164 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, C, B Time building chain proxies: 4.79, per 1000 atoms: 0.23 Number of scatterers: 20996 At special positions: 0 Unit cell: (151.2, 151.2, 148.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 40 16.00 O 3916 8.00 N 3876 7.00 C 13156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 904.6 milliseconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 16 sheets defined 75.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 81 through 100 removed outlier: 4.569A pdb=" N VAL A 87 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.759A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.875A pdb=" N LEU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 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 394 Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 600 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 removed outlier: 3.607A pdb=" N CYS A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 729 through 755 Processing helix chain 'A' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER A 764 " --> pdb=" O PRO A 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.286A pdb=" N MET A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA A 853 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 3.651A pdb=" N VAL A 872 " --> pdb=" O MET A 868 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.545A pdb=" N ARG A 907 " --> pdb=" O TRP A 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Proline residue: A 912 - end of helix removed outlier: 4.487A pdb=" N ILE A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 950 through 983 removed outlier: 3.660A pdb=" N MET A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1006 Processing helix chain 'A' and resid 1010 through 1028 removed outlier: 4.041A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A1028 " --> pdb=" O LYS A1024 " (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: 4.569A pdb=" N VAL D 87 " --> pdb=" O TRP D 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.758A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 removed outlier: 3.716A pdb=" N VAL D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL D 300 " --> pdb=" O TRP D 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.876A pdb=" N LEU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 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 394 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 528 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 542 through 560 removed outlier: 3.573A pdb=" N SER D 558 " --> pdb=" O ILE D 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 559 " --> pdb=" O LYS D 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 600 Processing helix chain 'D' and resid 610 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.658A pdb=" N GLN D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 655 removed outlier: 3.606A pdb=" N CYS D 655 " --> pdb=" O GLY D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 665 Processing helix chain 'D' and resid 717 through 728 Processing helix chain 'D' and resid 729 through 755 Processing helix chain 'D' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER D 764 " --> pdb=" O PRO D 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 766 " --> pdb=" O GLY D 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP D 773 " --> pdb=" O THR D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 804 removed outlier: 4.136A pdb=" N ASP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 821 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.285A pdb=" N MET D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE D 849 " --> pdb=" O THR D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA D 853 " --> pdb=" O HIS D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 895 removed outlier: 3.650A pdb=" N VAL D 872 " --> pdb=" O MET D 868 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 892 " --> pdb=" O VAL D 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 918 removed outlier: 3.544A pdb=" N ARG D 907 " --> pdb=" O TRP D 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 908 " --> pdb=" O ILE D 904 " (cutoff:3.500A) Proline residue: D 912 - end of helix removed outlier: 4.487A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE D 917 " --> pdb=" O TYR D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 930 Processing helix chain 'D' and resid 950 through 983 removed outlier: 3.659A pdb=" N MET D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 974 " --> pdb=" O MET D 970 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 975 " --> pdb=" O ASN D 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 1006 Processing helix chain 'D' and resid 1010 through 1028 removed outlier: 4.042A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D1028 " --> pdb=" O LYS D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' 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: 4.569A pdb=" N VAL C 87 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.758A pdb=" N ALA C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 238 through 250 removed outlier: 4.408A pdb=" N ARG C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.874A pdb=" N LEU C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 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 394 Processing helix chain 'C' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 515 through 528 Processing helix chain 'C' and resid 529 through 539 Processing helix chain 'C' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 Processing helix chain 'C' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 600 Processing helix chain 'C' and resid 610 through 618 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN C 629 " --> pdb=" O HIS C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 655 removed outlier: 3.608A pdb=" N CYS C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 665 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 729 through 755 Processing helix chain 'C' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER C 764 " --> pdb=" O PRO C 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP C 773 " --> pdb=" O THR C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 821 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.286A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE C 849 " --> pdb=" O THR C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA C 853 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 895 removed outlier: 3.651A pdb=" N VAL C 872 " --> pdb=" O MET C 868 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 892 " --> pdb=" O VAL C 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 918 removed outlier: 3.544A pdb=" N ARG C 907 " --> pdb=" O TRP C 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 908 " --> pdb=" O ILE C 904 " (cutoff:3.500A) Proline residue: C 912 - end of helix removed outlier: 4.487A pdb=" N ILE C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 950 through 983 removed outlier: 3.660A pdb=" N MET C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 974 " --> pdb=" O MET C 970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 975 " --> pdb=" O ASN C 971 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 983 " --> pdb=" O TYR C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1006 Processing helix chain 'C' and resid 1010 through 1028 removed outlier: 4.041A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C1028 " --> pdb=" O LYS C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' 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: 4.569A pdb=" N VAL B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.759A pdb=" N ALA B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL B 300 " --> pdb=" O TRP B 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.874A pdb=" N LEU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 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 394 Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN B 629 " --> pdb=" O HIS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 3.607A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 729 through 755 Processing helix chain 'B' and resid 760 through 787 removed outlier: 3.570A pdb=" N SER B 764 " --> pdb=" O PRO B 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 773 " --> pdb=" O THR B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 821 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.285A pdb=" N MET B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE B 849 " --> pdb=" O THR B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA B 853 " --> pdb=" O HIS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 3.652A pdb=" N VAL B 872 " --> pdb=" O MET B 868 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.546A pdb=" N ARG B 907 " --> pdb=" O TRP B 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Proline residue: B 912 - end of helix removed outlier: 4.488A pdb=" N ILE B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B 917 " --> pdb=" O TYR B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 950 through 983 removed outlier: 3.661A pdb=" N MET B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 974 " --> pdb=" O MET B 970 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 975 " --> pdb=" O ASN B 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1006 Processing helix chain 'B' and resid 1010 through 1028 removed outlier: 4.040A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B1028 " --> pdb=" O LYS B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS A 39 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 187 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 41 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA A 136 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 186 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 103 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET A 139 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 105 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER A 141 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 255 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA5, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS D 39 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 187 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 41 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA D 136 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE D 186 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE D 103 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 139 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 105 " --> pdb=" O MET D 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER D 141 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=AA7, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AA8, first strand: chain 'D' and resid 601 through 602 Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.674A pdb=" N LYS C 39 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU C 187 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 41 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA C 136 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 186 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 103 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET C 139 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 105 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER C 141 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AB2, first strand: chain 'C' and resid 253 through 255 Processing sheet with id=AB3, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS B 39 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU B 187 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 41 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA B 136 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE B 186 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 105 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER B 141 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB6, first strand: chain 'B' and resid 253 through 255 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 602 1788 hydrogen bonds defined for protein. 5280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.59 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: 7452 1.34 - 1.46: 4054 1.46 - 1.58: 9730 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 21292 Sorted by residual: bond pdb=" C LEU D 969 " pdb=" N MET D 970 " ideal model delta sigma weight residual 1.333 1.417 -0.084 1.26e-02 6.30e+03 4.45e+01 bond pdb=" C LEU C 969 " pdb=" N MET C 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C LEU A 969 " pdb=" N MET A 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C LEU B 969 " pdb=" N MET B 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C TRP C 992 " pdb=" N LYS C 993 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.32e-02 5.74e+03 6.06e+00 ... (remaining 21287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 27978 1.13 - 2.27: 1175 2.27 - 3.40: 175 3.40 - 4.54: 68 4.54 - 5.67: 20 Bond angle restraints: 29416 Sorted by residual: angle pdb=" CA ARG D 911 " pdb=" C ARG D 911 " pdb=" N PRO D 912 " ideal model delta sigma weight residual 120.93 116.10 4.83 1.06e+00 8.90e-01 2.07e+01 angle pdb=" CA ARG A 911 " pdb=" C ARG A 911 " pdb=" N PRO A 912 " ideal model delta sigma weight residual 120.93 116.11 4.82 1.06e+00 8.90e-01 2.06e+01 angle pdb=" CA ARG B 911 " pdb=" C ARG B 911 " pdb=" N PRO B 912 " ideal model delta sigma weight residual 120.93 116.12 4.81 1.06e+00 8.90e-01 2.06e+01 angle pdb=" CA ARG C 911 " pdb=" C ARG C 911 " pdb=" N PRO C 912 " ideal model delta sigma weight residual 120.93 116.14 4.79 1.06e+00 8.90e-01 2.04e+01 angle pdb=" N PRO D 759 " pdb=" CA PRO D 759 " pdb=" C PRO D 759 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.48e+00 ... (remaining 29411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 11452 12.00 - 24.00: 588 24.00 - 36.00: 152 36.00 - 48.00: 32 48.00 - 60.00: 16 Dihedral angle restraints: 12240 sinusoidal: 1844 harmonic: 10396 Sorted by residual: dihedral pdb=" CA PRO B 759 " pdb=" C PRO B 759 " pdb=" N PRO B 760 " pdb=" CA PRO B 760 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO A 759 " pdb=" C PRO A 759 " pdb=" N PRO A 760 " pdb=" CA PRO A 760 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO C 759 " pdb=" C PRO C 759 " pdb=" N PRO C 760 " pdb=" CA PRO C 760 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2382 0.027 - 0.054: 825 0.054 - 0.082: 363 0.082 - 0.109: 138 0.109 - 0.136: 32 Chirality restraints: 3740 Sorted by residual: chirality pdb=" CA ASN C 394 " pdb=" N ASN C 394 " pdb=" C ASN C 394 " pdb=" CB ASN C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ASN D 394 " pdb=" N ASN D 394 " pdb=" C ASN D 394 " pdb=" CB ASN D 394 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASN A 394 " pdb=" N ASN A 394 " pdb=" C ASN A 394 " pdb=" CB ASN A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 3737 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 759 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 760 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 759 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 760 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 759 " 0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO D 760 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 760 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 760 " 0.049 5.00e-02 4.00e+02 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1338 2.73 - 3.27: 25430 3.27 - 3.82: 35387 3.82 - 4.36: 35227 4.36 - 4.90: 55855 Nonbonded interactions: 153237 Sorted by model distance: nonbonded pdb=" O GLN D 761 " pdb=" OG SER D 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN A 761 " pdb=" OG SER A 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN B 761 " pdb=" OG SER B 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN C 761 " pdb=" OG SER C 764 " model vdw 2.188 3.040 nonbonded pdb=" O LEU C 421 " pdb=" OG SER C 424 " model vdw 2.192 3.040 ... (remaining 153232 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21292 Z= 0.226 Angle : 0.571 5.673 29416 Z= 0.370 Chirality : 0.037 0.136 3740 Planarity : 0.005 0.087 3956 Dihedral : 9.811 59.997 5376 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.13), residues: 3432 helix: -1.11 (0.10), residues: 2380 sheet: -2.86 (0.32), residues: 176 loop : -2.91 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 346 TYR 0.006 0.001 TYR D 997 PHE 0.013 0.001 PHE D 372 TRP 0.020 0.002 TRP C 378 HIS 0.009 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.23 (21292) covalent geometry : angle 0.57131 / 0.37 (29416) hydrogen bonds : bond 0.16036 / 11.89 ( 1788) hydrogen bonds : angle 6.23460 / 4.73 ( 5280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TRP cc_start: 0.8232 (m100) cc_final: 0.7798 (m100) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0555 time to fit residues: 4.8214 Evaluate side-chains 40 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 6.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 349 GLN A 737 ASN A 850 HIS A 855 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050983 restraints weight = 38990.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.051981 restraints weight = 27774.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052700 restraints weight = 21956.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053120 restraints weight = 18610.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053320 restraints weight = 16729.298| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21292 Z= 0.120 Angle : 0.460 5.247 29416 Z= 0.271 Chirality : 0.036 0.144 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.283 23.666 3552 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.43 % Allowed : 2.17 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3432 helix: 1.06 (0.10), residues: 2408 sheet: -2.34 (0.35), residues: 168 loop : -2.16 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 242 TYR 0.007 0.001 TYR C 587 PHE 0.014 0.001 PHE D 583 TRP 0.038 0.002 TRP A 773 HIS 0.004 0.001 HIS D 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.12 (21292) covalent geometry : angle 0.46017 / 0.27 (29416) hydrogen bonds : bond 0.03728 / 2.76 ( 1788) hydrogen bonds : angle 4.53596 / 3.43 ( 5280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.142 Fit side-chains REVERT: A 225 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6320 (mp10) REVERT: A 350 ASP cc_start: 0.9200 (t0) cc_final: 0.8993 (t0) REVERT: A 400 ARG cc_start: 0.9550 (ttm110) cc_final: 0.9272 (ttp80) REVERT: A 1062 LEU cc_start: 0.9845 (mt) cc_final: 0.9396 (mt) REVERT: A 1066 GLU cc_start: 0.9493 (tp30) cc_final: 0.9173 (tp30) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0413 time to fit residues: 3.6328 Evaluate side-chains 43 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 84 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 14 optimal weight: 0.0370 chunk 163 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 270 optimal weight: 0.0070 chunk 316 optimal weight: 9.9990 chunk 92 optimal weight: 0.0030 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 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 = 0.3489 r_free = 0.3489 target = 0.081108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055601 restraints weight = 38306.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053857 restraints weight = 31744.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053804 restraints weight = 29061.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.053950 restraints weight = 27212.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054047 restraints weight = 25004.944| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21292 Z= 0.098 Angle : 0.421 4.999 29416 Z= 0.243 Chirality : 0.035 0.127 3740 Planarity : 0.005 0.085 3956 Dihedral : 3.879 23.537 3552 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3432 helix: 1.93 (0.11), residues: 2408 sheet: -2.15 (0.34), residues: 192 loop : -1.67 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 242 TYR 0.024 0.002 TYR C 351 PHE 0.012 0.001 PHE A 536 TRP 0.025 0.001 TRP B 773 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.10 (21292) covalent geometry : angle 0.42126 / 0.24 (29416) hydrogen bonds : bond 0.02875 / 2.11 ( 1788) hydrogen bonds : angle 4.03808 / 3.06 ( 5280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9416 (t0) cc_final: 0.9123 (t0) REVERT: D 351 TYR cc_start: 0.8978 (m-80) cc_final: 0.8664 (m-80) REVERT: D 355 LEU cc_start: 0.9672 (tt) cc_final: 0.9458 (pp) REVERT: D 382 ASP cc_start: 0.8643 (m-30) cc_final: 0.8006 (p0) REVERT: D 400 ARG cc_start: 0.9518 (ttm110) cc_final: 0.9225 (ttm110) REVERT: D 810 ASP cc_start: 0.9029 (m-30) cc_final: 0.8824 (m-30) REVERT: D 996 ARG cc_start: 0.9734 (ttt180) cc_final: 0.9246 (ptm-80) REVERT: D 1062 LEU cc_start: 0.9827 (mt) cc_final: 0.9341 (mm) REVERT: D 1066 GLU cc_start: 0.9317 (tp30) cc_final: 0.9081 (pp20) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0535 time to fit residues: 4.6808 Evaluate side-chains 53 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 279 optimal weight: 40.0000 chunk 216 optimal weight: 9.9990 chunk 159 optimal weight: 0.0060 chunk 90 optimal weight: 50.0000 chunk 211 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 334 optimal weight: 8.9990 chunk 268 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.048906 restraints weight = 39508.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048908 restraints weight = 32540.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.048879 restraints weight = 27421.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.049710 restraints weight = 24224.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.049480 restraints weight = 22082.622| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21292 Z= 0.274 Angle : 0.577 11.384 29416 Z= 0.343 Chirality : 0.038 0.129 3740 Planarity : 0.005 0.088 3956 Dihedral : 4.348 22.737 3552 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3432 helix: 1.52 (0.10), residues: 2408 sheet: -2.02 (0.35), residues: 192 loop : -1.43 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 996 TYR 0.031 0.002 TYR B 351 PHE 0.024 0.002 PHE B 372 TRP 0.034 0.002 TRP B 773 HIS 0.009 0.003 HIS D 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.27 (21292) covalent geometry : angle 0.57706 / 0.34 (29416) hydrogen bonds : bond 0.03877 / 2.85 ( 1788) hydrogen bonds : angle 4.74192 / 3.58 ( 5280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9425 (t0) cc_final: 0.9212 (t0) REVERT: D 351 TYR cc_start: 0.9179 (m-80) cc_final: 0.8970 (m-80) REVERT: D 368 LYS cc_start: 0.9798 (mmmt) cc_final: 0.9501 (tptp) REVERT: D 400 ARG cc_start: 0.9544 (ttm110) cc_final: 0.9263 (ttm110) REVERT: D 996 ARG cc_start: 0.9830 (ttt180) cc_final: 0.9626 (ttm170) REVERT: D 1062 LEU cc_start: 0.9839 (mt) cc_final: 0.9529 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0521 time to fit residues: 3.7771 Evaluate side-chains 41 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 2 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 303 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 394 ASN D 737 ASN D 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050401 restraints weight = 40611.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049356 restraints weight = 34735.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.049460 restraints weight = 30200.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049573 restraints weight = 26507.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.049644 restraints weight = 24724.138| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21292 Z= 0.248 Angle : 0.540 7.452 29416 Z= 0.324 Chirality : 0.038 0.131 3740 Planarity : 0.005 0.086 3956 Dihedral : 4.496 23.665 3552 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.43 % Allowed : 2.17 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3432 helix: 1.41 (0.11), residues: 2412 sheet: -2.24 (0.33), residues: 192 loop : -1.26 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 346 TYR 0.038 0.002 TYR C 351 PHE 0.017 0.002 PHE D 372 TRP 0.031 0.002 TRP B 773 HIS 0.010 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.25 (21292) covalent geometry : angle 0.53959 / 0.32 (29416) hydrogen bonds : bond 0.03770 / 2.78 ( 1788) hydrogen bonds : angle 4.74641 / 3.58 ( 5280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9436 (t0) cc_final: 0.9209 (t0) REVERT: D 400 ARG cc_start: 0.9588 (ttm110) cc_final: 0.9279 (ttm110) REVERT: D 1062 LEU cc_start: 0.9842 (mt) cc_final: 0.9561 (mt) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0448 time to fit residues: 3.3282 Evaluate side-chains 40 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 294 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 212 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.077743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050956 restraints weight = 39272.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050122 restraints weight = 32417.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.050142 restraints weight = 29378.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.050143 restraints weight = 29453.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050646 restraints weight = 24547.100| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21292 Z= 0.132 Angle : 0.453 5.689 29416 Z= 0.264 Chirality : 0.036 0.156 3740 Planarity : 0.005 0.085 3956 Dihedral : 4.147 23.180 3552 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3432 helix: 1.84 (0.11), residues: 2452 sheet: -2.21 (0.37), residues: 168 loop : -1.15 (0.26), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 242 TYR 0.022 0.001 TYR C 351 PHE 0.013 0.001 PHE B 583 TRP 0.023 0.001 TRP A 773 HIS 0.009 0.001 HIS B 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (21292) covalent geometry : angle 0.45287 / 0.26 (29416) hydrogen bonds : bond 0.03051 / 2.25 ( 1788) hydrogen bonds : angle 4.22300 / 3.19 ( 5280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9492 (t0) cc_final: 0.9132 (t0) REVERT: D 400 ARG cc_start: 0.9565 (ttm110) cc_final: 0.9242 (ttm110) REVERT: D 810 ASP cc_start: 0.9140 (m-30) cc_final: 0.8875 (m-30) REVERT: D 1062 LEU cc_start: 0.9839 (mt) cc_final: 0.9536 (mt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0467 time to fit residues: 3.5101 Evaluate side-chains 41 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 267 optimal weight: 50.0000 chunk 219 optimal weight: 6.9990 chunk 349 optimal weight: 0.2980 chunk 197 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 299 optimal weight: 0.0470 chunk 216 optimal weight: 10.0000 overall best weight: 3.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050832 restraints weight = 39489.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.049678 restraints weight = 33368.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.049895 restraints weight = 29976.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049999 restraints weight = 26362.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.050146 restraints weight = 23614.092| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21292 Z= 0.180 Angle : 0.497 7.103 29416 Z= 0.290 Chirality : 0.037 0.159 3740 Planarity : 0.005 0.086 3956 Dihedral : 4.215 26.727 3552 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3432 helix: 1.92 (0.11), residues: 2388 sheet: -2.11 (0.39), residues: 168 loop : -1.08 (0.25), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.021 0.002 TYR C 351 PHE 0.017 0.001 PHE D 372 TRP 0.021 0.001 TRP B 773 HIS 0.008 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (21292) covalent geometry : angle 0.49704 / 0.29 (29416) hydrogen bonds : bond 0.03194 / 2.35 ( 1788) hydrogen bonds : angle 4.35806 / 3.29 ( 5280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.133 Fit side-chains REVERT: A 350 ASP cc_start: 0.9393 (t0) cc_final: 0.9119 (t0) REVERT: A 382 ASP cc_start: 0.8874 (m-30) cc_final: 0.8394 (p0) REVERT: A 400 ARG cc_start: 0.9563 (ttm110) cc_final: 0.9272 (ttm110) REVERT: A 810 ASP cc_start: 0.9240 (m-30) cc_final: 0.9018 (m-30) REVERT: A 970 MET cc_start: 0.8830 (ttt) cc_final: 0.8627 (tmm) REVERT: A 1062 LEU cc_start: 0.9836 (mt) cc_final: 0.9543 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0501 time to fit residues: 3.6998 Evaluate side-chains 41 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 320 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 285 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 268 optimal weight: 50.0000 chunk 259 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 349 GLN A 737 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049711 restraints weight = 39687.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.047886 restraints weight = 40565.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.048354 restraints weight = 33323.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.048403 restraints weight = 28621.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.048497 restraints weight = 26740.102| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21292 Z= 0.305 Angle : 0.604 10.473 29416 Z= 0.363 Chirality : 0.039 0.160 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.598 25.233 3552 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3432 helix: 1.35 (0.10), residues: 2408 sheet: -2.25 (0.43), residues: 108 loop : -1.24 (0.23), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 996 TYR 0.024 0.002 TYR B 351 PHE 0.021 0.002 PHE B 372 TRP 0.029 0.003 TRP B 992 HIS 0.013 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.31 (21292) covalent geometry : angle 0.60393 / 0.36 (29416) hydrogen bonds : bond 0.03908 / 2.87 ( 1788) hydrogen bonds : angle 4.86222 / 3.67 ( 5280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 350 ASP cc_start: 0.9345 (t0) cc_final: 0.9128 (t0) REVERT: A 400 ARG cc_start: 0.9590 (ttm110) cc_final: 0.9297 (ttm110) REVERT: A 810 ASP cc_start: 0.9210 (m-30) cc_final: 0.8992 (m-30) REVERT: A 1062 LEU cc_start: 0.9844 (mt) cc_final: 0.9530 (mt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0453 time to fit residues: 2.9278 Evaluate side-chains 38 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 172 optimal weight: 50.0000 chunk 202 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 350 optimal weight: 50.0000 chunk 291 optimal weight: 0.0270 chunk 289 optimal weight: 0.0170 chunk 127 optimal weight: 7.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN A 737 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.079532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052889 restraints weight = 38307.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.051870 restraints weight = 29583.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051852 restraints weight = 29950.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051948 restraints weight = 27071.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.052113 restraints weight = 24574.069| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21292 Z= 0.098 Angle : 0.460 5.680 29416 Z= 0.259 Chirality : 0.036 0.169 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.956 24.410 3552 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.15), residues: 3432 helix: 2.36 (0.11), residues: 2388 sheet: -2.37 (0.40), residues: 132 loop : -0.85 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 996 TYR 0.016 0.001 TYR A 351 PHE 0.012 0.001 PHE D 583 TRP 0.031 0.002 TRP C 992 HIS 0.005 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (21292) covalent geometry : angle 0.46034 / 0.26 (29416) hydrogen bonds : bond 0.02813 / 2.06 ( 1788) hydrogen bonds : angle 3.95120 / 2.99 ( 5280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 350 ASP cc_start: 0.9397 (t0) cc_final: 0.9072 (t0) REVERT: A 382 ASP cc_start: 0.8892 (m-30) cc_final: 0.8451 (p0) REVERT: A 400 ARG cc_start: 0.9563 (ttm110) cc_final: 0.9252 (ttm110) REVERT: A 1062 LEU cc_start: 0.9822 (mt) cc_final: 0.9479 (mm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0393 time to fit residues: 3.5817 Evaluate side-chains 48 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 141 optimal weight: 8.9990 chunk 327 optimal weight: 3.9990 chunk 176 optimal weight: 0.0670 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 40.0000 chunk 303 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 251 optimal weight: 50.0000 chunk 348 optimal weight: 6.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.077888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051637 restraints weight = 38809.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.050327 restraints weight = 36158.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050681 restraints weight = 29678.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.050827 restraints weight = 25741.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050938 restraints weight = 24052.154| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21292 Z= 0.139 Angle : 0.467 6.333 29416 Z= 0.268 Chirality : 0.036 0.157 3740 Planarity : 0.005 0.085 3956 Dihedral : 3.936 23.599 3552 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.15), residues: 3432 helix: 2.41 (0.11), residues: 2392 sheet: -2.12 (0.44), residues: 108 loop : -0.82 (0.23), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 242 TYR 0.023 0.002 TYR C 587 PHE 0.014 0.001 PHE A 372 TRP 0.022 0.002 TRP B 992 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (21292) covalent geometry : angle 0.46660 / 0.27 (29416) hydrogen bonds : bond 0.02752 / 2.02 ( 1788) hydrogen bonds : angle 4.01537 / 3.04 ( 5280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9467 (t0) cc_final: 0.9215 (t0) REVERT: D 382 ASP cc_start: 0.8786 (m-30) cc_final: 0.8237 (p0) REVERT: D 400 ARG cc_start: 0.9552 (ttm110) cc_final: 0.9226 (ttm110) REVERT: D 1062 LEU cc_start: 0.9826 (mt) cc_final: 0.9524 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0389 time to fit residues: 3.2550 Evaluate side-chains 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 277 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 350 optimal weight: 40.0000 chunk 312 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 191 optimal weight: 50.0000 chunk 286 optimal weight: 5.9990 chunk 109 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 349 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 = 0.3385 r_free = 0.3385 target = 0.075685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049815 restraints weight = 40087.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.048628 restraints weight = 34317.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.048779 restraints weight = 30146.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048845 restraints weight = 27539.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048989 restraints weight = 25571.705| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21292 Z= 0.277 Angle : 0.577 9.355 29416 Z= 0.344 Chirality : 0.039 0.157 3740 Planarity : 0.005 0.086 3956 Dihedral : 4.319 24.041 3552 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3432 helix: 1.84 (0.11), residues: 2396 sheet: -2.23 (0.44), residues: 108 loop : -1.04 (0.23), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 996 TYR 0.026 0.003 TYR A 587 PHE 0.023 0.002 PHE A 372 TRP 0.021 0.002 TRP B 992 HIS 0.011 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.28 (21292) covalent geometry : angle 0.57681 / 0.34 (29416) hydrogen bonds : bond 0.03615 / 2.65 ( 1788) hydrogen bonds : angle 4.58989 / 3.46 ( 5280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.87 seconds wall clock time: 29 minutes 37.81 seconds (1777.81 seconds total)