Starting phenix.real_space_refine on Wed Jun 18 12:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sli_40578/06_2025/8sli_40578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sli_40578/06_2025/8sli_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_40578/06_2025/8sli_40578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sli_40578/06_2025/8sli_40578.map" model { file = "/net/cci-nas-00/data/ceres_data/8sli_40578/06_2025/8sli_40578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sli_40578/06_2025/8sli_40578.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 24, 'ASP:plan': 36, 'TYR:plan': 16, 'ASN:plan1': 13, 'TRP:plan': 12, 'HIS:plan': 13, 'PHE:plan': 34, 'GLU:plan': 48, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 1164 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 13.35, per 1000 atoms: 0.64 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: 5.89 Conformation dependent library (CDL) restraints added in 3.6 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: 3.07 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: 8.54 Time building geometry restraints manager: 6.91 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 52.470 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP C 378 HIS 0.009 0.001 HIS D 998 PHE 0.013 0.001 PHE D 372 TYR 0.006 0.001 TYR D 997 ARG 0.005 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.16036 ( 1788) hydrogen bonds : angle 6.23460 ( 5280) covalent geometry : bond 0.00363 (21292) covalent geometry : angle 0.57131 (29416) *********************** 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 : 0.513 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: 0.1512 time to fit residues: 12.7528 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 8.9990 chunk 269 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 0.0060 chunk 323 optimal weight: 2.9990 overall best weight: 3.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN B 349 GLN B 850 HIS ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.076922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050890 restraints weight = 39135.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049954 restraints weight = 30420.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.049643 restraints weight = 27739.399| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21292 Z= 0.193 Angle : 0.514 5.490 29416 Z= 0.306 Chirality : 0.037 0.153 3740 Planarity : 0.005 0.089 3956 Dihedral : 4.607 23.484 3552 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3432 helix: 0.55 (0.10), residues: 2416 sheet: -2.40 (0.35), residues: 168 loop : -2.28 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 773 HIS 0.007 0.002 HIS D 612 PHE 0.016 0.001 PHE B 372 TYR 0.007 0.001 TYR A 587 ARG 0.002 0.001 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1788) hydrogen bonds : angle 4.96920 ( 5280) covalent geometry : bond 0.00335 (21292) covalent geometry : angle 0.51424 (29416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ASP cc_start: 0.9364 (t0) cc_final: 0.9143 (t0) REVERT: B 400 ARG cc_start: 0.9562 (ttm110) cc_final: 0.9340 (ttm110) REVERT: B 810 ASP cc_start: 0.8930 (m-30) cc_final: 0.8727 (m-30) REVERT: B 976 MET cc_start: 0.7852 (mmp) cc_final: 0.7436 (ppp) REVERT: B 1062 LEU cc_start: 0.9895 (mt) cc_final: 0.9506 (mt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1278 time to fit residues: 10.1898 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 : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 278 optimal weight: 50.0000 chunk 308 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 177 optimal weight: 0.5980 chunk 291 optimal weight: 0.0470 chunk 251 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 270 optimal weight: 0.9990 chunk 179 optimal weight: 50.0000 chunk 79 optimal weight: 5.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 ASN A 855 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.078779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051925 restraints weight = 38729.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.050826 restraints weight = 38916.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051433 restraints weight = 31631.448| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2020 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= 0.120 Angle : 0.426 5.126 29416 Z= 0.249 Chirality : 0.035 0.130 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.061 23.765 3552 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3432 helix: 1.45 (0.10), residues: 2408 sheet: -2.32 (0.34), residues: 192 loop : -1.83 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 773 HIS 0.003 0.001 HIS D 612 PHE 0.016 0.001 PHE C 744 TYR 0.015 0.001 TYR B 587 ARG 0.001 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 1788) hydrogen bonds : angle 4.28778 ( 5280) covalent geometry : bond 0.00209 (21292) covalent geometry : angle 0.42551 (29416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.546 Fit side-chains REVERT: A 351 TYR cc_start: 0.9017 (m-10) cc_final: 0.8812 (m-80) REVERT: A 382 ASP cc_start: 0.8809 (m-30) cc_final: 0.8305 (p0) REVERT: A 400 ARG cc_start: 0.9559 (ttm110) cc_final: 0.9304 (ttm110) REVERT: A 996 ARG cc_start: 0.9776 (ttt180) cc_final: 0.9208 (ptm-80) REVERT: A 1062 LEU cc_start: 0.9835 (mt) cc_final: 0.9477 (mt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1325 time to fit residues: 10.2124 Evaluate side-chains 44 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 258 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 205 optimal weight: 0.0170 chunk 243 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 296 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 112 optimal weight: 30.0000 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3446 r_free = 0.3446 target = 0.078687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053003 restraints weight = 39346.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.051949 restraints weight = 32626.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.052140 restraints weight = 27108.816| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2312 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= 0.122 Angle : 0.437 8.042 29416 Z= 0.252 Chirality : 0.036 0.122 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.931 23.490 3552 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3432 helix: 1.75 (0.11), residues: 2384 sheet: -2.10 (0.35), residues: 192 loop : -1.43 (0.24), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 773 HIS 0.004 0.001 HIS B 612 PHE 0.010 0.001 PHE D 412 TYR 0.016 0.001 TYR C 587 ARG 0.001 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 1788) hydrogen bonds : angle 4.13999 ( 5280) covalent geometry : bond 0.00224 (21292) covalent geometry : angle 0.43710 (29416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9541 (ttm110) cc_final: 0.9245 (ttm110) REVERT: D 996 ARG cc_start: 0.9767 (ttt180) cc_final: 0.9200 (ptm160) REVERT: D 1062 LEU cc_start: 0.9822 (mt) cc_final: 0.9335 (mm) REVERT: D 1066 GLU cc_start: 0.9320 (tp30) cc_final: 0.9041 (pp20) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1337 time to fit residues: 10.6875 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 : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 230 optimal weight: 8.9990 chunk 266 optimal weight: 0.6980 chunk 55 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 270 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051272 restraints weight = 39154.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049886 restraints weight = 32718.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050108 restraints weight = 28782.858| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21292 Z= 0.202 Angle : 0.497 7.636 29416 Z= 0.292 Chirality : 0.037 0.122 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.169 24.085 3552 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3432 helix: 1.06 (0.10), residues: 2400 sheet: -2.24 (0.34), residues: 192 loop : -1.64 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 773 HIS 0.008 0.002 HIS D 612 PHE 0.017 0.001 PHE A 372 TYR 0.037 0.002 TYR C 351 ARG 0.003 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 1788) hydrogen bonds : angle 4.41706 ( 5280) covalent geometry : bond 0.00351 (21292) covalent geometry : angle 0.49674 (29416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.9111 (m-80) cc_final: 0.8718 (m-80) REVERT: A 400 ARG cc_start: 0.9565 (ttm110) cc_final: 0.9290 (ttm110) REVERT: A 810 ASP cc_start: 0.9232 (m-30) cc_final: 0.9002 (m-30) REVERT: A 1062 LEU cc_start: 0.9833 (mt) cc_final: 0.9547 (mt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1341 time to fit residues: 9.5757 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 : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 195 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 247 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3351 r_free = 0.3351 target = 0.073434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048689 restraints weight = 40018.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.047181 restraints weight = 38527.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.047438 restraints weight = 32002.466| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21292 Z= 0.330 Angle : 0.670 12.950 29416 Z= 0.396 Chirality : 0.040 0.186 3740 Planarity : 0.006 0.087 3956 Dihedral : 5.188 24.530 3552 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.02 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3432 helix: -0.28 (0.10), residues: 2408 sheet: -2.59 (0.34), residues: 192 loop : -2.06 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 773 HIS 0.018 0.003 HIS B 612 PHE 0.027 0.002 PHE D 464 TYR 0.044 0.003 TYR B 351 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1788) hydrogen bonds : angle 5.44354 ( 5280) covalent geometry : bond 0.00565 (21292) covalent geometry : angle 0.67013 (29416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.632 Fit side-chains REVERT: A 400 ARG cc_start: 0.9611 (ttm110) cc_final: 0.9353 (ttp80) REVERT: A 1062 LEU cc_start: 0.9856 (mt) cc_final: 0.9587 (mt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1207 time to fit residues: 7.8541 Evaluate side-chains 35 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050194 restraints weight = 39146.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.048603 restraints weight = 37271.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048990 restraints weight = 30117.572| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21292 Z= 0.175 Angle : 0.481 5.318 29416 Z= 0.283 Chirality : 0.036 0.128 3740 Planarity : 0.005 0.088 3956 Dihedral : 4.450 26.195 3552 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3432 helix: 0.61 (0.10), residues: 2424 sheet: -2.89 (0.37), residues: 156 loop : -1.80 (0.24), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 773 HIS 0.006 0.001 HIS A 612 PHE 0.016 0.001 PHE B 583 TYR 0.026 0.002 TYR B 351 ARG 0.003 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 1788) hydrogen bonds : angle 4.55841 ( 5280) covalent geometry : bond 0.00310 (21292) covalent geometry : angle 0.48107 (29416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 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 : 0.577 Fit side-chains REVERT: A 400 ARG cc_start: 0.9561 (ttm110) cc_final: 0.9267 (ttm110) REVERT: A 1062 LEU cc_start: 0.9849 (mt) cc_final: 0.9572 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1060 time to fit residues: 7.9421 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 298 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 50.0000 chunk 249 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 231 optimal weight: 0.0370 chunk 213 optimal weight: 0.0020 chunk 329 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.8468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052747 restraints weight = 38215.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052440 restraints weight = 30302.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052168 restraints weight = 26440.042| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3382 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= 0.089 Angle : 0.421 6.105 29416 Z= 0.239 Chirality : 0.035 0.122 3740 Planarity : 0.005 0.085 3956 Dihedral : 3.826 24.245 3552 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3432 helix: 1.48 (0.10), residues: 2368 sheet: -3.14 (0.33), residues: 132 loop : -1.61 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 773 HIS 0.009 0.001 HIS B 850 PHE 0.010 0.001 PHE B 583 TYR 0.015 0.001 TYR C 351 ARG 0.001 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.02594 ( 1788) hydrogen bonds : angle 3.92339 ( 5280) covalent geometry : bond 0.00175 (21292) covalent geometry : angle 0.42088 (29416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 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 : 0.530 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9551 (ttm110) cc_final: 0.9219 (ttm110) REVERT: D 996 ARG cc_start: 0.9445 (ttt90) cc_final: 0.9235 (ptm160) REVERT: D 1062 LEU cc_start: 0.9826 (mt) cc_final: 0.9495 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1103 time to fit residues: 9.2931 Evaluate side-chains 44 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 117 optimal weight: 10.0000 chunk 300 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 100 optimal weight: 50.0000 chunk 325 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.077455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050642 restraints weight = 38797.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.049957 restraints weight = 35189.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049823 restraints weight = 33057.357| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21292 Z= 0.159 Angle : 0.488 8.557 29416 Z= 0.273 Chirality : 0.036 0.121 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.897 24.276 3552 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3432 helix: 1.40 (0.10), residues: 2372 sheet: -3.13 (0.31), residues: 168 loop : -1.36 (0.24), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 773 HIS 0.007 0.002 HIS A 612 PHE 0.016 0.001 PHE D 372 TYR 0.024 0.002 TYR D 587 ARG 0.001 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 1788) hydrogen bonds : angle 4.10269 ( 5280) covalent geometry : bond 0.00291 (21292) covalent geometry : angle 0.48847 (29416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 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 : 0.563 Fit side-chains REVERT: A 316 LEU cc_start: 0.8471 (pp) cc_final: 0.8259 (mm) REVERT: A 382 ASP cc_start: 0.8853 (m-30) cc_final: 0.8429 (p0) REVERT: A 400 ARG cc_start: 0.9568 (ttm110) cc_final: 0.9272 (ttm110) REVERT: A 1062 LEU cc_start: 0.9831 (mt) cc_final: 0.9550 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1309 time to fit residues: 10.1764 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 186 optimal weight: 50.0000 chunk 343 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 265 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 202 optimal weight: 0.0170 chunk 197 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 overall best weight: 1.0416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052850 restraints weight = 38440.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051649 restraints weight = 30789.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.051798 restraints weight = 29370.941| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3649 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= 0.089 Angle : 0.427 6.016 29416 Z= 0.238 Chirality : 0.036 0.154 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.665 24.379 3552 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3432 helix: 1.72 (0.10), residues: 2364 sheet: -3.19 (0.30), residues: 168 loop : -1.37 (0.24), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 773 HIS 0.004 0.001 HIS D 998 PHE 0.012 0.001 PHE D 841 TYR 0.016 0.001 TYR C 351 ARG 0.001 0.000 ARG A 996 Details of bonding type rmsd hydrogen bonds : bond 0.02484 ( 1788) hydrogen bonds : angle 3.82089 ( 5280) covalent geometry : bond 0.00178 (21292) covalent geometry : angle 0.42739 (29416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 382 ASP cc_start: 0.8848 (m-30) cc_final: 0.8386 (p0) REVERT: A 400 ARG cc_start: 0.9566 (ttm110) cc_final: 0.9239 (ttm110) REVERT: A 1062 LEU cc_start: 0.9819 (mt) cc_final: 0.9531 (mt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1041 time to fit residues: 9.2310 Evaluate side-chains 45 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 295 optimal weight: 9.9990 chunk 19 optimal weight: 0.0010 chunk 102 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 8 optimal weight: 0.0980 chunk 335 optimal weight: 0.3980 overall best weight: 0.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051775 restraints weight = 38132.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052782 restraints weight = 27400.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053542 restraints weight = 21729.860| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3866 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= 0.082 Angle : 0.416 6.647 29416 Z= 0.227 Chirality : 0.035 0.116 3740 Planarity : 0.004 0.085 3956 Dihedral : 3.446 24.450 3552 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3432 helix: 1.81 (0.10), residues: 2364 sheet: -3.16 (0.30), residues: 168 loop : -1.36 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 773 HIS 0.004 0.001 HIS D 998 PHE 0.012 0.001 PHE B 994 TYR 0.024 0.001 TYR B 587 ARG 0.001 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.02171 ( 1788) hydrogen bonds : angle 3.59093 ( 5280) covalent geometry : bond 0.00163 (21292) covalent geometry : angle 0.41575 (29416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.60 seconds wall clock time: 63 minutes 52.46 seconds (3832.46 seconds total)