Starting phenix.real_space_refine on Sat Jul 4 13:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sli_40578/07_2026/8sli_40578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sli_40578/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sli_40578/07_2026/8sli_40578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sli_40578/07_2026/8sli_40578.map" model { file = "/net/cci-nas-00/data/ceres_data/8sli_40578/07_2026/8sli_40578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sli_40578/07_2026/8sli_40578.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: D, C, B Time building chain proxies: 5.30, per 1000 atoms: 0.25 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 4.23 Time building geometry restraints manager: 2.78 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: 0.06 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.220 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 : 0.125 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: 0.0452 time to fit residues: 3.8667 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 : 0.150 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050835 restraints weight = 38994.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.051785 restraints weight = 27786.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052291 restraints weight = 22091.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052927 restraints weight = 19179.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053216 restraints weight = 17108.665| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21292 Z= 0.121 Angle : 0.462 5.249 29416 Z= 0.272 Chirality : 0.036 0.143 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.291 23.687 3552 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: 0.10 (0.15), residues: 3432 helix: 1.04 (0.10), residues: 2408 sheet: -2.36 (0.35), residues: 168 loop : -2.18 (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 A 587 PHE 0.015 0.001 PHE D 583 TRP 0.037 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 0.46180 / 0.27 (29416) hydrogen bonds : bond 0.03781 / 2.80 ( 1788) hydrogen bonds : angle 4.56687 / 3.45 ( 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 59 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.194 Fit side-chains REVERT: A 350 ASP cc_start: 0.9330 (t0) cc_final: 0.9032 (t0) REVERT: A 400 ARG cc_start: 0.9547 (ttm110) cc_final: 0.9272 (ttm110) REVERT: A 1062 LEU cc_start: 0.9845 (mt) cc_final: 0.9393 (mt) REVERT: A 1066 GLU cc_start: 0.9449 (tp30) cc_final: 0.9120 (tp30) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0510 time to fit residues: 4.4431 Evaluate side-chains 42 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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: 0.9990 chunk 155 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 163 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 326 optimal weight: 20.0000 chunk 270 optimal weight: 0.5980 chunk 316 optimal weight: 9.9990 chunk 92 optimal weight: 0.0270 overall best weight: 0.9252 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.080342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054674 restraints weight = 38333.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053233 restraints weight = 30344.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053033 restraints weight = 28786.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.053145 restraints weight = 27422.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053263 restraints weight = 25012.311| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2179 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= 0.101 Angle : 0.427 5.065 29416 Z= 0.248 Chirality : 0.035 0.126 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.959 23.471 3552 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 1.19 (0.15), residues: 3432 helix: 1.86 (0.11), residues: 2408 sheet: -2.16 (0.34), residues: 192 loop : -1.72 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 346 TYR 0.034 0.002 TYR B 351 PHE 0.011 0.001 PHE B 583 TRP 0.027 0.001 TRP B 773 HIS 0.003 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.10 (21292) covalent geometry : angle 0.42718 / 0.25 (29416) hydrogen bonds : bond 0.02967 / 2.18 ( 1788) hydrogen bonds : angle 4.14181 / 3.13 ( 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 56 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9545 (t0) cc_final: 0.9157 (t0) REVERT: D 351 TYR cc_start: 0.8963 (m-80) cc_final: 0.8602 (m-80) REVERT: D 355 LEU cc_start: 0.9669 (tt) cc_final: 0.9463 (pp) REVERT: D 400 ARG cc_start: 0.9526 (ttm110) cc_final: 0.9247 (ttm110) REVERT: D 996 ARG cc_start: 0.9754 (ttt180) cc_final: 0.9179 (ptm-80) REVERT: D 1062 LEU cc_start: 0.9828 (mt) cc_final: 0.9462 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0554 time to fit residues: 4.4518 Evaluate side-chains 46 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 50.0000 chunk 216 optimal weight: 7.9990 chunk 159 optimal weight: 0.0570 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: 3.9990 chunk 212 optimal weight: 7.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.075794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.050282 restraints weight = 39247.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048862 restraints weight = 31967.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.048694 restraints weight = 28708.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.048861 restraints weight = 27677.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049046 restraints weight = 24796.535| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21292 Z= 0.266 Angle : 0.570 10.822 29416 Z= 0.339 Chirality : 0.038 0.139 3740 Planarity : 0.005 0.088 3956 Dihedral : 4.412 22.817 3552 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: 0.83 (0.15), residues: 3432 helix: 1.46 (0.10), residues: 2424 sheet: -2.04 (0.35), residues: 192 loop : -1.50 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 996 TYR 0.031 0.002 TYR C 351 PHE 0.024 0.002 PHE C 372 TRP 0.032 0.002 TRP C 773 HIS 0.009 0.002 HIS D 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.27 (21292) covalent geometry : angle 0.57017 / 0.34 (29416) hydrogen bonds : bond 0.03856 / 2.83 ( 1788) hydrogen bonds : angle 4.75591 / 3.59 ( 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 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9536 (t0) cc_final: 0.9167 (t0) REVERT: D 368 LYS cc_start: 0.9764 (mmtt) cc_final: 0.9458 (tptp) REVERT: D 400 ARG cc_start: 0.9556 (ttm110) cc_final: 0.9286 (ttm110) REVERT: D 996 ARG cc_start: 0.9817 (ttt180) cc_final: 0.9611 (ttm170) REVERT: D 1062 LEU cc_start: 0.9845 (mt) cc_final: 0.9565 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0429 time to fit residues: 2.9357 Evaluate side-chains 39 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 90 optimal weight: 40.0000 chunk 85 optimal weight: 6.9990 chunk 303 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 394 ASN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.047655 restraints weight = 41237.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.046148 restraints weight = 39188.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046806 restraints weight = 33226.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046795 restraints weight = 27147.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.046902 restraints weight = 25605.404| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21292 Z= 0.364 Angle : 0.693 12.719 29416 Z= 0.418 Chirality : 0.041 0.176 3740 Planarity : 0.006 0.087 3956 Dihedral : 5.270 25.710 3552 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.43 % Allowed : 5.22 % Favored : 94.35 % 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: -0.22 (0.15), residues: 3432 helix: 0.59 (0.10), residues: 2404 sheet: -2.27 (0.35), residues: 192 loop : -1.57 (0.24), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 996 TYR 0.045 0.003 TYR B 351 PHE 0.030 0.003 PHE B 464 TRP 0.035 0.003 TRP A 773 HIS 0.020 0.003 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.36 (21292) covalent geometry : angle 0.69310 / 0.42 (29416) hydrogen bonds : bond 0.04900 / 3.60 ( 1788) hydrogen bonds : angle 5.52930 / 4.17 ( 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 45 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.213 Fit side-chains REVERT: D 350 ASP cc_start: 0.9571 (t0) cc_final: 0.9305 (t0) REVERT: D 400 ARG cc_start: 0.9619 (ttm110) cc_final: 0.9306 (ttm110) REVERT: D 997 TYR cc_start: 0.9652 (t80) cc_final: 0.9440 (t80) REVERT: D 1062 LEU cc_start: 0.9854 (mt) cc_final: 0.9573 (mt) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0462 time to fit residues: 3.0062 Evaluate side-chains 36 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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: 8.9990 chunk 297 optimal weight: 0.0870 chunk 298 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 229 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 784 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 = 0.3396 r_free = 0.3396 target = 0.075794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050255 restraints weight = 39633.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.049001 restraints weight = 35081.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.049093 restraints weight = 30841.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.049164 restraints weight = 29172.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.049333 restraints weight = 24904.041| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21292 Z= 0.187 Angle : 0.516 5.717 29416 Z= 0.302 Chirality : 0.037 0.166 3740 Planarity : 0.005 0.085 3956 Dihedral : 4.575 27.225 3552 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 0.75 (0.15), residues: 3432 helix: 1.39 (0.11), residues: 2404 sheet: -2.36 (0.38), residues: 168 loop : -1.37 (0.25), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.019 0.001 TYR D 351 PHE 0.017 0.001 PHE A 583 TRP 0.026 0.002 TRP D 773 HIS 0.007 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.19 (21292) covalent geometry : angle 0.51640 / 0.30 (29416) hydrogen bonds : bond 0.03598 / 2.65 ( 1788) hydrogen bonds : angle 4.69171 / 3.54 ( 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 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.180 Fit side-chains REVERT: A 350 ASP cc_start: 0.9586 (t0) cc_final: 0.9269 (t0) REVERT: A 382 ASP cc_start: 0.8922 (m-30) cc_final: 0.8462 (p0) REVERT: A 400 ARG cc_start: 0.9587 (ttm110) cc_final: 0.9295 (ttm110) REVERT: A 1062 LEU cc_start: 0.9841 (mt) cc_final: 0.9593 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0407 time to fit residues: 3.0570 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 : 0.173 ------------------------------------------------------------------------------- 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: 0.6980 chunk 197 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 309 optimal weight: 0.4980 chunk 4 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 299 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 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 = 0.3398 r_free = 0.3398 target = 0.076406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051473 restraints weight = 39642.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049942 restraints weight = 35103.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050221 restraints weight = 31168.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050255 restraints weight = 27636.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.050289 restraints weight = 26030.806| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3220 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= 0.189 Angle : 0.520 7.577 29416 Z= 0.304 Chirality : 0.037 0.162 3740 Planarity : 0.005 0.085 3956 Dihedral : 4.461 26.134 3552 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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: 1.07 (0.15), residues: 3432 helix: 1.62 (0.11), residues: 2384 sheet: -2.64 (0.41), residues: 128 loop : -1.17 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.023 0.002 TYR C 351 PHE 0.017 0.001 PHE A 372 TRP 0.022 0.002 TRP A 773 HIS 0.008 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.19 (21292) covalent geometry : angle 0.52045 / 0.30 (29416) hydrogen bonds : bond 0.03491 / 2.58 ( 1788) hydrogen bonds : angle 4.58352 / 3.46 ( 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 : 0.206 Fit side-chains revert: symmetry clash REVERT: D 350 ASP cc_start: 0.9611 (t0) cc_final: 0.9378 (t0) REVERT: D 400 ARG cc_start: 0.9574 (ttm110) cc_final: 0.9261 (ttm110) REVERT: D 1062 LEU cc_start: 0.9834 (mt) cc_final: 0.9557 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0559 time to fit residues: 4.0730 Evaluate side-chains 42 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 0.1980 chunk 31 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 127 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 268 optimal weight: 50.0000 chunk 259 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 784 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 = 0.3409 r_free = 0.3409 target = 0.076985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050861 restraints weight = 39233.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.049127 restraints weight = 33857.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.049981 restraints weight = 30823.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049941 restraints weight = 25764.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.050016 restraints weight = 25666.602| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21292 Z= 0.162 Angle : 0.490 6.377 29416 Z= 0.284 Chirality : 0.037 0.163 3740 Planarity : 0.005 0.085 3956 Dihedral : 4.281 25.488 3552 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: 1.43 (0.15), residues: 3432 helix: 1.89 (0.11), residues: 2392 sheet: -2.40 (0.44), residues: 108 loop : -1.15 (0.23), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 242 TYR 0.021 0.001 TYR A 351 PHE 0.015 0.001 PHE A 372 TRP 0.019 0.001 TRP A 773 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (21292) covalent geometry : angle 0.48971 / 0.28 (29416) hydrogen bonds : bond 0.03194 / 2.35 ( 1788) hydrogen bonds : angle 4.38859 / 3.32 ( 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 51 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9550 (ttm110) cc_final: 0.9214 (ttm110) REVERT: D 1062 LEU cc_start: 0.9835 (mt) cc_final: 0.9546 (mt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0424 time to fit residues: 3.3518 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 : 0.217 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 172 optimal weight: 50.0000 chunk 202 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 350 optimal weight: 50.0000 chunk 291 optimal weight: 0.0870 chunk 289 optimal weight: 0.0870 chunk 127 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.5940 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.078671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.050027 restraints weight = 38253.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050917 restraints weight = 27880.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051624 restraints weight = 22361.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052014 restraints weight = 19201.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052344 restraints weight = 17371.132| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3633 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= 0.104 Angle : 0.455 7.113 29416 Z= 0.258 Chirality : 0.036 0.160 3740 Planarity : 0.005 0.085 3956 Dihedral : 3.953 24.224 3552 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: 1.99 (0.15), residues: 3432 helix: 2.34 (0.11), residues: 2408 sheet: -2.56 (0.42), residues: 128 loop : -0.97 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 242 TYR 0.019 0.001 TYR D 351 PHE 0.011 0.001 PHE A 583 TRP 0.040 0.002 TRP C 773 HIS 0.005 0.001 HIS D 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (21292) covalent geometry : angle 0.45549 / 0.26 (29416) hydrogen bonds : bond 0.02716 / 2.00 ( 1788) hydrogen bonds : angle 3.99891 / 3.03 ( 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 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: D 400 ARG cc_start: 0.9550 (ttm110) cc_final: 0.9251 (ttm110) REVERT: D 1062 LEU cc_start: 0.9812 (mt) cc_final: 0.9507 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0413 time to fit residues: 3.4874 Evaluate side-chains 42 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 1.9990 chunk 176 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 172 optimal weight: 50.0000 chunk 303 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 251 optimal weight: 40.0000 chunk 348 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.050943 restraints weight = 39171.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048967 restraints weight = 33376.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.048559 restraints weight = 31449.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.048547 restraints weight = 34891.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.048774 restraints weight = 28607.054| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21292 Z= 0.238 Angle : 0.563 8.948 29416 Z= 0.328 Chirality : 0.039 0.160 3740 Planarity : 0.005 0.085 3956 Dihedral : 4.325 24.025 3552 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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: 1.52 (0.15), residues: 3432 helix: 1.93 (0.11), residues: 2396 sheet: -2.38 (0.45), residues: 108 loop : -1.04 (0.23), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 996 TYR 0.028 0.002 TYR B 351 PHE 0.020 0.002 PHE A 372 TRP 0.055 0.002 TRP B 773 HIS 0.011 0.003 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.24 (21292) covalent geometry : angle 0.56339 / 0.33 (29416) hydrogen bonds : bond 0.03463 / 2.54 ( 1788) hydrogen bonds : angle 4.52253 / 3.42 ( 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 48 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9557 (ttm110) cc_final: 0.9285 (ttm110) REVERT: D 1062 LEU cc_start: 0.9847 (mt) cc_final: 0.9519 (mt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0391 time to fit residues: 3.0001 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 : 0.127 ------------------------------------------------------------------------------- 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: 50.0000 chunk 312 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 336 optimal weight: 0.0970 chunk 135 optimal weight: 10.0000 chunk 191 optimal weight: 50.0000 chunk 286 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 overall best weight: 3.8782 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.076954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052683 restraints weight = 39518.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.051443 restraints weight = 34174.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.051400 restraints weight = 33353.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.051193 restraints weight = 33081.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.051295 restraints weight = 27687.132| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21292 Z= 0.185 Angle : 0.510 6.641 29416 Z= 0.296 Chirality : 0.038 0.164 3740 Planarity : 0.005 0.086 3956 Dihedral : 4.243 24.504 3552 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3432 helix: 2.02 (0.11), residues: 2388 sheet: -2.45 (0.45), residues: 108 loop : -1.04 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 242 TYR 0.025 0.002 TYR B 351 PHE 0.016 0.001 PHE C 372 TRP 0.052 0.002 TRP D 773 HIS 0.007 0.001 HIS D 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.19 (21292) covalent geometry : angle 0.51040 / 0.30 (29416) hydrogen bonds : bond 0.03195 / 2.35 ( 1788) hydrogen bonds : angle 4.33718 / 3.28 ( 5280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.58 seconds wall clock time: 29 minutes 14.54 seconds (1754.54 seconds total)