Starting phenix.real_space_refine on Mon Sep 30 08:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f9y_50263/09_2024/9f9y_50263.cif" } resolution = 2.8 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= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15834 2.51 5 N 4050 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "B" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.71, per 1000 atoms: 0.67 Number of scatterers: 24810 At special positions: 0 Unit cell: (128.533, 129.993, 171.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4818 8.00 N 4050 7.00 C 15834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 735 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A1007 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A1057 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 735 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B1007 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B1057 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 276 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 500 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 513 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 624 " distance=2.03 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 735 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C1007 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C1057 " - pdb=" SG CYS C1101 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 49 " " NAG A1302 " - " ASN A 108 " " NAG A1303 " - " ASN A 140 " " NAG A1304 " - " ASN A 163 " " NAG A1305 " - " ASN A 209 " " NAG A1306 " - " ASN A 257 " " NAG A1307 " - " ASN A 306 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 591 " " NAG A1310 " - " ASN A 632 " " NAG A1311 " - " ASN A 684 " " NAG A1312 " - " ASN A1049 " " NAG A1313 " - " ASN A1109 " " NAG B1301 " - " ASN B 49 " " NAG B1302 " - " ASN B 108 " " NAG B1303 " - " ASN B 140 " " NAG B1304 " - " ASN B 163 " " NAG B1305 " - " ASN B 209 " " NAG B1306 " - " ASN B 257 " " NAG B1307 " - " ASN B 306 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 591 " " NAG B1310 " - " ASN B 632 " " NAG B1311 " - " ASN B 684 " " NAG B1312 " - " ASN B1049 " " NAG B1313 " - " ASN B1109 " " NAG C1301 " - " ASN C 49 " " NAG C1302 " - " ASN C 108 " " NAG C1303 " - " ASN C 140 " " NAG C1304 " - " ASN C 163 " " NAG C1305 " - " ASN C 209 " " NAG C1306 " - " ASN C 257 " " NAG C1307 " - " ASN C 306 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 591 " " NAG C1310 " - " ASN C 632 " " NAG C1311 " - " ASN C 684 " " NAG C1312 " - " ASN C1049 " " NAG C1313 " - " ASN C1109 " " NAG D 1 " - " ASN A 692 " " NAG E 1 " - " ASN A 776 " " NAG F 1 " - " ASN A1073 " " NAG G 1 " - " ASN B 692 " " NAG H 1 " - " ASN B 776 " " NAG I 1 " - " ASN B1073 " " NAG J 1 " - " ASN C 692 " " NAG K 1 " - " ASN C 776 " " NAG L 1 " - " ASN C1073 " Time building additional restraints: 6.98 Conformation dependent library (CDL) restraints added in 3.2 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 29.1% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.532A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.637A pdb=" N VAL A 342 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.529A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER A 383 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 612 through 615 removed outlier: 6.611A pdb=" N SER A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.584A pdb=" N ASP A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 801 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 841 through 860 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 887 through 894 removed outlier: 4.079A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 916 removed outlier: 3.934A pdb=" N GLN A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.608A pdb=" N GLN A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 951 through 959 Processing helix chain 'A' and resid 960 through 1008 removed outlier: 4.711A pdb=" N VAL A 966 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 974 " --> pdb=" O ARG A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 removed outlier: 4.118A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.536A pdb=" N VAL B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.633A pdb=" N VAL B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.533A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.666A pdb=" N VAL B 610 " --> pdb=" O PRO B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 712 through 719 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 801 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 841 through 860 Processing helix chain 'B' and resid 861 through 865 Processing helix chain 'B' and resid 872 through 884 Processing helix chain 'B' and resid 887 through 894 removed outlier: 4.085A pdb=" N LEU B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 911 " --> pdb=" O GLY B 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 940 removed outlier: 3.602A pdb=" N GLN B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 943 No H-bonds generated for 'chain 'B' and resid 941 through 943' Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 1008 removed outlier: 4.730A pdb=" N VAL B 966 " --> pdb=" O PRO B 962 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 974 " --> pdb=" O ARG B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1122 removed outlier: 4.119A pdb=" N GLU B1119 " --> pdb=" O PRO B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.537A pdb=" N VAL C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.638A pdb=" N VAL C 342 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.528A pdb=" N LEU C 362 " --> pdb=" O PRO C 359 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER C 383 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 477 through 480 Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.659A pdb=" N VAL C 610 " --> pdb=" O PRO C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 712 through 719 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP C 750 " --> pdb=" O ALA C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 801 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 841 through 860 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 872 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.092A pdb=" N LEU C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN C 910 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 911 " --> pdb=" O GLY C 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 940 removed outlier: 3.603A pdb=" N GLN C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 943 No H-bonds generated for 'chain 'C' and resid 941 through 943' Processing helix chain 'C' and resid 951 through 959 Processing helix chain 'C' and resid 960 through 1008 removed outlier: 4.707A pdb=" N VAL C 966 " --> pdb=" O PRO C 962 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1122 removed outlier: 4.117A pdb=" N GLU C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 8.020A pdb=" N ASN A 49 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A 244 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 180 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N HIS A 182 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LEU A 198 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 24 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 43 removed outlier: 4.031A pdb=" N ASP A 262 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.550A pdb=" N SER A 137 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 294 removed outlier: 4.299A pdb=" N VAL A 570 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN A 292 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 568 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY A 569 " --> pdb=" O GLN A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 removed outlier: 5.458A pdb=" N ASP A 549 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 541 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 333 removed outlier: 3.727A pdb=" N ASN A 369 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 351 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.686A pdb=" N CYS A 336 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 630 removed outlier: 6.024A pdb=" N GLU A 629 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 671 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 647 " --> pdb=" O PRO A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 690 removed outlier: 3.795A pdb=" N ALA A1053 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A1070 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 703 removed outlier: 6.974A pdb=" N GLY A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A1030 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1036 " --> pdb=" O PRO A1028 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1038 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1026 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1040 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 711 removed outlier: 4.464A pdb=" N LYS A 708 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 763 through 765 removed outlier: 5.848A pdb=" N ILE A 763 " --> pdb=" O ASN B 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN B 49 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 244 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 180 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N HIS B 182 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU B 198 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 24 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 35 through 43 removed outlier: 4.026A pdb=" N ASP B 262 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.545A pdb=" N SER B 137 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 294 removed outlier: 4.307A pdb=" N VAL B 570 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN B 292 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 568 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 569 " --> pdb=" O GLN B 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 303 removed outlier: 5.449A pdb=" N ASP B 549 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B 541 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN B 369 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 351 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.689A pdb=" N CYS B 336 " --> pdb=" O CYS B 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 630 removed outlier: 6.028A pdb=" N GLU B 629 " --> pdb=" O ALA B 669 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 671 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 686 through 690 removed outlier: 3.834A pdb=" N ALA B1053 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B1070 " --> pdb=" O ALA B1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 703 removed outlier: 6.985A pdb=" N GLY B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B1030 " --> pdb=" O GLY B1034 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1036 " --> pdb=" O PRO B1028 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B1038 " --> pdb=" O SER B1026 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B1026 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B1040 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 711 removed outlier: 4.478A pdb=" N LYS B 708 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.824A pdb=" N ILE B 763 " --> pdb=" O ASN C 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN C 49 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR C 244 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER C 180 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N HIS C 182 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU C 198 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 24 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 35 through 43 removed outlier: 4.029A pdb=" N ASP C 262 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.551A pdb=" N SER C 137 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 286 through 294 removed outlier: 4.306A pdb=" N VAL C 570 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN C 292 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 568 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C 569 " --> pdb=" O GLN C 588 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 300 through 303 removed outlier: 5.453A pdb=" N ASP C 549 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 541 " --> pdb=" O ASP C 549 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN C 369 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 351 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 336 through 337 removed outlier: 6.683A pdb=" N CYS C 336 " --> pdb=" O CYS C 500 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AE7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AE8, first strand: chain 'C' and resid 628 through 630 removed outlier: 6.016A pdb=" N GLU C 629 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 671 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 686 through 690 removed outlier: 3.843A pdb=" N ALA C1053 " --> pdb=" O PHE C1070 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE C1070 " --> pdb=" O ALA C1053 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 693 through 703 removed outlier: 6.992A pdb=" N GLY C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER C1030 " --> pdb=" O GLY C1034 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1036 " --> pdb=" O PRO C1028 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C1038 " --> pdb=" O SER C1026 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C1026 " --> pdb=" O LEU C1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C1040 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 708 through 711 removed outlier: 4.477A pdb=" N LYS C 708 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1095 through 1097 1065 hydrogen bonds defined for protein. 2847 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: 12.90 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7826 1.34 - 1.46: 6034 1.46 - 1.58: 11379 1.58 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 25374 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 33426 1.32 - 2.63: 868 2.63 - 3.95: 201 3.95 - 5.26: 20 5.26 - 6.58: 6 Bond angle restraints: 34521 Sorted by residual: angle pdb=" N ALA C 598 " pdb=" CA ALA C 598 " pdb=" C ALA C 598 " ideal model delta sigma weight residual 111.11 114.11 -3.00 1.20e+00 6.94e-01 6.27e+00 angle pdb=" N ALA B 598 " pdb=" CA ALA B 598 " pdb=" C ALA B 598 " ideal model delta sigma weight residual 111.11 114.04 -2.93 1.20e+00 6.94e-01 5.96e+00 angle pdb=" C SER A 596 " pdb=" N VAL A 597 " pdb=" CA VAL A 597 " ideal model delta sigma weight residual 120.46 123.48 -3.02 1.37e+00 5.33e-01 4.86e+00 angle pdb=" N PRO A 961 " pdb=" CA PRO A 961 " pdb=" C PRO A 961 " ideal model delta sigma weight residual 110.70 113.33 -2.63 1.22e+00 6.72e-01 4.66e+00 angle pdb=" N PRO C 961 " pdb=" CA PRO C 961 " pdb=" C PRO C 961 " ideal model delta sigma weight residual 110.70 113.32 -2.62 1.22e+00 6.72e-01 4.61e+00 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15060 17.58 - 35.16: 610 35.16 - 52.73: 93 52.73 - 70.31: 45 70.31 - 87.89: 17 Dihedral angle restraints: 15825 sinusoidal: 6882 harmonic: 8943 Sorted by residual: dihedral pdb=" CA THR B 574 " pdb=" C THR B 574 " pdb=" N PRO B 575 " pdb=" CA PRO B 575 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 574 " pdb=" C THR A 574 " pdb=" N PRO A 575 " pdb=" CA PRO A 575 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 574 " pdb=" C THR C 574 " pdb=" N PRO C 575 " pdb=" CA PRO C 575 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2350 0.029 - 0.058: 1057 0.058 - 0.087: 319 0.087 - 0.116: 290 0.116 - 0.144: 64 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 4077 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 605 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 606 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 606 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 606 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 605 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO B 606 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 606 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 606 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 605 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 606 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.022 5.00e-02 4.00e+02 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5759 2.79 - 3.32: 22578 3.32 - 3.84: 40041 3.84 - 4.37: 48421 4.37 - 4.90: 83598 Nonbonded interactions: 200397 Sorted by model distance: nonbonded pdb=" O GLN C 120 " pdb=" OG SER C 136 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 120 " pdb=" OG SER A 136 " model vdw 2.262 3.040 nonbonded pdb=" O GLN B 120 " pdb=" OG SER B 136 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 608 " pdb=" OG SER A 612 " model vdw 2.293 3.040 nonbonded pdb=" O PRO A1028 " pdb=" NE2 GLN A1029 " model vdw 2.306 3.120 ... (remaining 200392 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 2.870 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 64.550 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 0.036 25374 Z= 0.265 Angle : 0.519 6.576 34521 Z= 0.256 Chirality : 0.044 0.144 4080 Planarity : 0.003 0.068 4380 Dihedral : 10.390 87.887 9960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.52 % Allowed : 4.04 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3036 helix: 1.93 (0.20), residues: 732 sheet: 0.58 (0.18), residues: 735 loop : -0.63 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.003 0.000 HIS C1039 PHE 0.009 0.001 PHE C1096 TYR 0.017 0.001 TYR B1042 ARG 0.003 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 143 PHE cc_start: 0.8597 (t80) cc_final: 0.8361 (t80) REVERT: A 284 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8656 (p90) REVERT: A 349 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6645 (p90) REVERT: A 416 LEU cc_start: 0.9207 (mt) cc_final: 0.8673 (tt) REVERT: A 600 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: A 715 MET cc_start: 0.9080 (tpp) cc_final: 0.8763 (tpt) REVERT: A 798 PHE cc_start: 0.8398 (t80) cc_final: 0.8071 (t80) REVERT: A 831 ASN cc_start: 0.8414 (m-40) cc_final: 0.8120 (m-40) REVERT: A 969 ASP cc_start: 0.8593 (t70) cc_final: 0.8293 (t0) REVERT: A 1120 LEU cc_start: 0.7590 (pp) cc_final: 0.7277 (pp) REVERT: B 101 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 143 PHE cc_start: 0.8617 (t80) cc_final: 0.8254 (t80) REVERT: B 284 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8830 (p90) REVERT: B 349 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7437 (p90) REVERT: B 416 LEU cc_start: 0.9186 (mt) cc_final: 0.8603 (tt) REVERT: B 706 MET cc_start: 0.9645 (ptt) cc_final: 0.9416 (ptt) REVERT: B 831 ASN cc_start: 0.8439 (m-40) cc_final: 0.8145 (m-40) REVERT: B 969 ASP cc_start: 0.8691 (t70) cc_final: 0.8330 (t0) REVERT: B 1120 LEU cc_start: 0.7726 (pp) cc_final: 0.7397 (pp) REVERT: C 326 TYR cc_start: 0.9062 (p90) cc_final: 0.8733 (p90) REVERT: C 349 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6763 (p90) REVERT: C 358 SER cc_start: 0.8430 (m) cc_final: 0.8031 (p) REVERT: C 730 GLN cc_start: 0.9020 (tt0) cc_final: 0.8809 (tt0) REVERT: C 798 PHE cc_start: 0.8478 (t80) cc_final: 0.8188 (t80) REVERT: C 831 ASN cc_start: 0.8460 (m-40) cc_final: 0.8145 (m-40) REVERT: C 969 ASP cc_start: 0.8641 (t70) cc_final: 0.8316 (t0) REVERT: C 1120 LEU cc_start: 0.7690 (pp) cc_final: 0.7367 (pp) outliers start: 14 outliers final: 6 residues processed: 271 average time/residue: 1.1041 time to fit residues: 356.0013 Evaluate side-chains 179 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0030 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 120 GLN A 139 ASN A 193 GLN A 494 HIS ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN A 932 GLN A 985 GLN B 18 ASN B 120 GLN B 139 ASN B 494 HIS B 600 HIS B 665 GLN B 730 GLN B 932 GLN B 985 GLN C 18 ASN C 120 GLN C 139 ASN C 494 HIS C 600 HIS C 665 GLN C 730 GLN C 932 GLN C 985 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 25374 Z= 0.371 Angle : 0.560 11.040 34521 Z= 0.285 Chirality : 0.045 0.180 4080 Planarity : 0.004 0.072 4380 Dihedral : 6.723 59.580 4505 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.39 % Allowed : 7.27 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.15), residues: 3036 helix: 1.69 (0.20), residues: 735 sheet: 0.62 (0.18), residues: 720 loop : -0.73 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.005 0.001 HIS B 600 PHE 0.020 0.001 PHE C 143 TYR 0.019 0.001 TYR B1042 ARG 0.006 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7657 (mm-40) REVERT: A 284 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8264 (mm-30) REVERT: A 326 TYR cc_start: 0.9115 (p90) cc_final: 0.8767 (p90) REVERT: A 345 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8179 (p0) REVERT: A 349 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 416 LEU cc_start: 0.9219 (mt) cc_final: 0.8718 (tt) REVERT: A 427 MET cc_start: 0.7478 (mpp) cc_final: 0.7129 (mpp) REVERT: A 715 MET cc_start: 0.9090 (tpp) cc_final: 0.8838 (tpt) REVERT: A 798 PHE cc_start: 0.8394 (t80) cc_final: 0.8150 (t80) REVERT: A 831 ASN cc_start: 0.8473 (m-40) cc_final: 0.8187 (m-40) REVERT: A 969 ASP cc_start: 0.8617 (t70) cc_final: 0.8326 (t0) REVERT: B 101 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7628 (mm-40) REVERT: B 143 PHE cc_start: 0.8627 (t80) cc_final: 0.8243 (t80) REVERT: B 284 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 326 TYR cc_start: 0.9137 (p90) cc_final: 0.8922 (p90) REVERT: B 345 ASN cc_start: 0.8436 (m110) cc_final: 0.8110 (p0) REVERT: B 346 PHE cc_start: 0.7413 (t80) cc_final: 0.7159 (t80) REVERT: B 349 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7361 (p90) REVERT: B 377 ILE cc_start: 0.8746 (tp) cc_final: 0.8538 (tp) REVERT: B 416 LEU cc_start: 0.9178 (mt) cc_final: 0.8621 (tt) REVERT: B 427 MET cc_start: 0.7518 (mpp) cc_final: 0.7244 (mpp) REVERT: B 831 ASN cc_start: 0.8467 (m-40) cc_final: 0.8149 (m-40) REVERT: B 969 ASP cc_start: 0.8711 (t70) cc_final: 0.8364 (t0) REVERT: C 326 TYR cc_start: 0.9107 (p90) cc_final: 0.8832 (p90) REVERT: C 345 ASN cc_start: 0.8386 (m110) cc_final: 0.8074 (p0) REVERT: C 346 PHE cc_start: 0.7517 (t80) cc_final: 0.7214 (t80) REVERT: C 349 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6788 (p90) REVERT: C 377 ILE cc_start: 0.8663 (tp) cc_final: 0.8434 (tp) REVERT: C 416 LEU cc_start: 0.9076 (mt) cc_final: 0.8491 (tt) REVERT: C 427 MET cc_start: 0.7530 (mpp) cc_final: 0.7218 (mpp) REVERT: C 621 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8199 (ttp-110) REVERT: C 798 PHE cc_start: 0.8464 (t80) cc_final: 0.8115 (m-80) REVERT: C 831 ASN cc_start: 0.8493 (m-40) cc_final: 0.8195 (m-40) REVERT: C 969 ASP cc_start: 0.8660 (t70) cc_final: 0.8331 (t0) REVERT: C 970 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8607 (ttp-170) outliers start: 37 outliers final: 16 residues processed: 205 average time/residue: 1.0851 time to fit residues: 265.7454 Evaluate side-chains 185 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 345 ASN A 600 HIS A 730 GLN A 985 GLN B 18 ASN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25374 Z= 0.211 Angle : 0.511 10.158 34521 Z= 0.257 Chirality : 0.043 0.176 4080 Planarity : 0.004 0.072 4380 Dihedral : 5.873 59.971 4502 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.95 % Allowed : 7.27 % Favored : 90.79 % 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: 0.44 (0.15), residues: 3036 helix: 1.96 (0.20), residues: 711 sheet: 0.70 (0.19), residues: 663 loop : -0.62 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.003 0.000 HIS C 600 PHE 0.024 0.001 PHE C 143 TYR 0.017 0.001 TYR A1042 ARG 0.005 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8835 (t0) cc_final: 0.8566 (t70) REVERT: A 101 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7704 (mm-40) REVERT: A 284 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8261 (mm-30) REVERT: A 309 ASN cc_start: 0.6933 (OUTLIER) cc_final: 0.6638 (p0) REVERT: A 326 TYR cc_start: 0.9128 (p90) cc_final: 0.8750 (p90) REVERT: A 349 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.6592 (p90) REVERT: A 416 LEU cc_start: 0.9217 (mt) cc_final: 0.8721 (tt) REVERT: A 427 MET cc_start: 0.7639 (mpp) cc_final: 0.7277 (mpp) REVERT: A 561 ASP cc_start: 0.8005 (t0) cc_final: 0.7691 (t0) REVERT: A 715 MET cc_start: 0.9066 (tpp) cc_final: 0.8850 (tpt) REVERT: A 798 PHE cc_start: 0.8358 (t80) cc_final: 0.8131 (t80) REVERT: A 831 ASN cc_start: 0.8421 (m-40) cc_final: 0.8118 (m-40) REVERT: A 969 ASP cc_start: 0.8578 (t70) cc_final: 0.8280 (t0) REVERT: A 980 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: B 41 ASP cc_start: 0.8868 (t0) cc_final: 0.8639 (t70) REVERT: B 101 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7665 (mm-40) REVERT: B 143 PHE cc_start: 0.8611 (t80) cc_final: 0.8200 (t80) REVERT: B 326 TYR cc_start: 0.9164 (p90) cc_final: 0.8917 (p90) REVERT: B 345 ASN cc_start: 0.8427 (m110) cc_final: 0.8095 (p0) REVERT: B 346 PHE cc_start: 0.7540 (t80) cc_final: 0.7333 (t80) REVERT: B 349 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7290 (p90) REVERT: B 416 LEU cc_start: 0.9163 (mt) cc_final: 0.8611 (tt) REVERT: B 427 MET cc_start: 0.7673 (mpp) cc_final: 0.7393 (mpp) REVERT: B 561 ASP cc_start: 0.8134 (t0) cc_final: 0.7863 (t0) REVERT: B 831 ASN cc_start: 0.8460 (m-40) cc_final: 0.8156 (m-40) REVERT: B 969 ASP cc_start: 0.8652 (t70) cc_final: 0.8325 (t0) REVERT: C 41 ASP cc_start: 0.8839 (t0) cc_final: 0.8590 (t70) REVERT: C 326 TYR cc_start: 0.9119 (p90) cc_final: 0.8813 (p90) REVERT: C 349 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.6770 (p90) REVERT: C 353 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7812 (ttmm) REVERT: C 416 LEU cc_start: 0.9087 (mt) cc_final: 0.8518 (tt) REVERT: C 427 MET cc_start: 0.7639 (mpp) cc_final: 0.7312 (mpp) REVERT: C 621 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8173 (ttp-110) REVERT: C 798 PHE cc_start: 0.8409 (t80) cc_final: 0.8097 (m-80) REVERT: C 831 ASN cc_start: 0.8486 (m-40) cc_final: 0.8163 (m-40) REVERT: C 969 ASP cc_start: 0.8587 (t70) cc_final: 0.8243 (t0) outliers start: 52 outliers final: 20 residues processed: 209 average time/residue: 1.0165 time to fit residues: 257.5933 Evaluate side-chains 192 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1116 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 25374 Z= 0.420 Angle : 0.565 10.843 34521 Z= 0.285 Chirality : 0.045 0.158 4080 Planarity : 0.004 0.074 4380 Dihedral : 5.624 57.800 4501 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 7.53 % Favored : 90.34 % 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: 3036 helix: 1.92 (0.20), residues: 693 sheet: 0.48 (0.19), residues: 702 loop : -0.70 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1077 HIS 0.011 0.001 HIS A 600 PHE 0.026 0.002 PHE A 346 TYR 0.019 0.001 TYR A1042 ARG 0.003 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7681 (mm-40) REVERT: A 284 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8256 (mm-30) REVERT: A 309 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (p0) REVERT: A 326 TYR cc_start: 0.9118 (p90) cc_final: 0.8760 (p90) REVERT: A 349 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.6684 (p90) REVERT: A 416 LEU cc_start: 0.9223 (mt) cc_final: 0.8702 (tt) REVERT: A 427 MET cc_start: 0.7693 (mpp) cc_final: 0.7349 (mpp) REVERT: A 561 ASP cc_start: 0.8043 (t0) cc_final: 0.7831 (t0) REVERT: A 798 PHE cc_start: 0.8402 (t80) cc_final: 0.8133 (t80) REVERT: A 831 ASN cc_start: 0.8480 (m-40) cc_final: 0.8197 (m-40) REVERT: A 969 ASP cc_start: 0.8611 (t70) cc_final: 0.8349 (t0) REVERT: B 41 ASP cc_start: 0.8897 (t0) cc_final: 0.8668 (t70) REVERT: B 101 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7631 (mm-40) REVERT: B 143 PHE cc_start: 0.8582 (t80) cc_final: 0.8135 (t80) REVERT: B 326 TYR cc_start: 0.9167 (p90) cc_final: 0.8935 (p90) REVERT: B 349 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7272 (p90) REVERT: B 416 LEU cc_start: 0.9176 (mt) cc_final: 0.8638 (tp) REVERT: B 427 MET cc_start: 0.7784 (mpp) cc_final: 0.7486 (mpp) REVERT: B 561 ASP cc_start: 0.8160 (t0) cc_final: 0.7908 (t0) REVERT: B 831 ASN cc_start: 0.8491 (m-40) cc_final: 0.8174 (m-40) REVERT: B 969 ASP cc_start: 0.8718 (t70) cc_final: 0.8375 (t0) REVERT: C 101 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7704 (mm-40) REVERT: C 326 TYR cc_start: 0.9122 (p90) cc_final: 0.8800 (p90) REVERT: C 349 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.6847 (p90) REVERT: C 353 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7733 (ttmm) REVERT: C 416 LEU cc_start: 0.9109 (mt) cc_final: 0.8550 (tt) REVERT: C 427 MET cc_start: 0.7707 (mpp) cc_final: 0.7367 (mpp) REVERT: C 621 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8181 (ttp-110) REVERT: C 798 PHE cc_start: 0.8450 (t80) cc_final: 0.8055 (m-80) REVERT: C 831 ASN cc_start: 0.8501 (m-40) cc_final: 0.8206 (m-40) REVERT: C 969 ASP cc_start: 0.8657 (t70) cc_final: 0.8327 (t0) outliers start: 57 outliers final: 23 residues processed: 205 average time/residue: 0.9848 time to fit residues: 246.0541 Evaluate side-chains 190 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Chi-restraints excluded: chain C residue 1116 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25374 Z= 0.225 Angle : 0.514 9.729 34521 Z= 0.258 Chirality : 0.044 0.168 4080 Planarity : 0.004 0.073 4380 Dihedral : 5.107 55.012 4501 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.25 % Allowed : 8.01 % Favored : 89.74 % 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: 0.39 (0.15), residues: 3036 helix: 1.92 (0.20), residues: 705 sheet: 0.59 (0.19), residues: 669 loop : -0.62 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 411 HIS 0.003 0.000 HIS C 600 PHE 0.031 0.001 PHE B 346 TYR 0.017 0.001 TYR A1042 ARG 0.005 0.000 ARG C 970 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 179 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8872 (t0) cc_final: 0.8570 (t70) REVERT: A 67 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7070 (p0) REVERT: A 101 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7654 (mm-40) REVERT: A 116 VAL cc_start: 0.8193 (m) cc_final: 0.7839 (p) REVERT: A 284 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8251 (mm-30) REVERT: A 309 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6914 (p0) REVERT: A 326 TYR cc_start: 0.9121 (p90) cc_final: 0.8770 (p90) REVERT: A 349 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6696 (p90) REVERT: A 416 LEU cc_start: 0.9208 (mt) cc_final: 0.8704 (tt) REVERT: A 427 MET cc_start: 0.7682 (mpp) cc_final: 0.7306 (mpp) REVERT: A 561 ASP cc_start: 0.8040 (t0) cc_final: 0.7630 (t0) REVERT: A 621 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8226 (ttp-110) REVERT: A 798 PHE cc_start: 0.8350 (t80) cc_final: 0.8115 (t80) REVERT: A 831 ASN cc_start: 0.8442 (m-40) cc_final: 0.8121 (m-40) REVERT: A 969 ASP cc_start: 0.8588 (t70) cc_final: 0.8309 (t0) REVERT: A 980 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: B 41 ASP cc_start: 0.8881 (t0) cc_final: 0.8674 (t70) REVERT: B 67 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7046 (p0) REVERT: B 101 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7676 (mm-40) REVERT: B 116 VAL cc_start: 0.8175 (m) cc_final: 0.7901 (p) REVERT: B 143 PHE cc_start: 0.8568 (t80) cc_final: 0.8181 (t80) REVERT: B 326 TYR cc_start: 0.9174 (p90) cc_final: 0.8906 (p90) REVERT: B 349 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7334 (p90) REVERT: B 416 LEU cc_start: 0.9178 (mt) cc_final: 0.8623 (tt) REVERT: B 427 MET cc_start: 0.7811 (mpp) cc_final: 0.7493 (mpp) REVERT: B 561 ASP cc_start: 0.8127 (t0) cc_final: 0.7825 (t0) REVERT: B 831 ASN cc_start: 0.8455 (m-40) cc_final: 0.8129 (m-40) REVERT: B 969 ASP cc_start: 0.8673 (t70) cc_final: 0.8352 (t0) REVERT: B 980 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: C 41 ASP cc_start: 0.8859 (t0) cc_final: 0.8602 (t70) REVERT: C 67 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7299 (p0) REVERT: C 101 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7747 (mm-40) REVERT: C 326 TYR cc_start: 0.9118 (p90) cc_final: 0.8756 (p90) REVERT: C 349 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.6868 (p90) REVERT: C 416 LEU cc_start: 0.9123 (mt) cc_final: 0.8577 (tt) REVERT: C 427 MET cc_start: 0.7675 (mpp) cc_final: 0.7292 (mpp) REVERT: C 621 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8159 (ttp-110) REVERT: C 798 PHE cc_start: 0.8411 (t80) cc_final: 0.8035 (m-80) REVERT: C 831 ASN cc_start: 0.8497 (m-40) cc_final: 0.8169 (m-40) REVERT: C 969 ASP cc_start: 0.8622 (t70) cc_final: 0.8283 (t0) outliers start: 60 outliers final: 28 residues processed: 215 average time/residue: 1.0012 time to fit residues: 260.9978 Evaluate side-chains 205 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25374 Z= 0.247 Angle : 0.515 9.298 34521 Z= 0.259 Chirality : 0.044 0.154 4080 Planarity : 0.004 0.072 4380 Dihedral : 4.805 49.435 4498 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 8.54 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3036 helix: 2.13 (0.20), residues: 684 sheet: 0.47 (0.19), residues: 690 loop : -0.65 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 411 HIS 0.003 0.000 HIS C 600 PHE 0.031 0.001 PHE B 346 TYR 0.017 0.001 TYR A1042 ARG 0.003 0.000 ARG C 970 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8876 (t0) cc_final: 0.8580 (t70) REVERT: A 87 ILE cc_start: 0.9320 (tp) cc_final: 0.8993 (pp) REVERT: A 101 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7638 (mm-40) REVERT: A 116 VAL cc_start: 0.8213 (m) cc_final: 0.7865 (p) REVERT: A 284 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8250 (mm-30) REVERT: A 326 TYR cc_start: 0.9110 (p90) cc_final: 0.8707 (p90) REVERT: A 349 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6762 (p90) REVERT: A 416 LEU cc_start: 0.9211 (mt) cc_final: 0.8705 (tt) REVERT: A 427 MET cc_start: 0.7699 (mpp) cc_final: 0.7382 (mpp) REVERT: A 561 ASP cc_start: 0.8044 (t0) cc_final: 0.7796 (t0) REVERT: A 621 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8214 (ttp-110) REVERT: A 798 PHE cc_start: 0.8356 (t80) cc_final: 0.8134 (t80) REVERT: A 831 ASN cc_start: 0.8432 (m-40) cc_final: 0.8088 (m-40) REVERT: A 969 ASP cc_start: 0.8586 (t70) cc_final: 0.8326 (t0) REVERT: B 41 ASP cc_start: 0.8894 (t0) cc_final: 0.8670 (t70) REVERT: B 67 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7058 (p0) REVERT: B 87 ILE cc_start: 0.9367 (tp) cc_final: 0.8980 (pp) REVERT: B 101 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7678 (mm-40) REVERT: B 116 VAL cc_start: 0.8187 (m) cc_final: 0.7906 (p) REVERT: B 143 PHE cc_start: 0.8555 (t80) cc_final: 0.8163 (t80) REVERT: B 326 TYR cc_start: 0.9177 (p90) cc_final: 0.8896 (p90) REVERT: B 349 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7337 (p90) REVERT: B 416 LEU cc_start: 0.9195 (mt) cc_final: 0.8650 (tt) REVERT: B 427 MET cc_start: 0.7820 (mpp) cc_final: 0.7481 (mpp) REVERT: B 561 ASP cc_start: 0.8126 (t0) cc_final: 0.7844 (t0) REVERT: B 831 ASN cc_start: 0.8467 (m-40) cc_final: 0.8153 (m-40) REVERT: B 969 ASP cc_start: 0.8670 (t70) cc_final: 0.8339 (t0) REVERT: B 980 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: C 41 ASP cc_start: 0.8869 (t0) cc_final: 0.8627 (t70) REVERT: C 101 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7719 (mm-40) REVERT: C 326 TYR cc_start: 0.9136 (p90) cc_final: 0.8813 (p90) REVERT: C 349 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6825 (p90) REVERT: C 416 LEU cc_start: 0.9173 (mt) cc_final: 0.8637 (tt) REVERT: C 427 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: C 621 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8151 (ttp-110) REVERT: C 798 PHE cc_start: 0.8424 (t80) cc_final: 0.8049 (m-80) REVERT: C 831 ASN cc_start: 0.8479 (m-40) cc_final: 0.8158 (m-40) REVERT: C 969 ASP cc_start: 0.8619 (t70) cc_final: 0.8353 (t0) outliers start: 52 outliers final: 29 residues processed: 212 average time/residue: 1.0445 time to fit residues: 270.4763 Evaluate side-chains 198 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25374 Z= 0.182 Angle : 0.502 9.761 34521 Z= 0.252 Chirality : 0.043 0.173 4080 Planarity : 0.003 0.071 4380 Dihedral : 4.529 46.838 4498 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 9.25 % Favored : 88.91 % 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: 0.47 (0.15), residues: 3036 helix: 2.06 (0.20), residues: 702 sheet: 0.61 (0.19), residues: 660 loop : -0.57 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.002 0.000 HIS C 600 PHE 0.032 0.001 PHE B 346 TYR 0.016 0.001 TYR A1042 ARG 0.003 0.000 ARG C 970 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8837 (t0) cc_final: 0.8523 (t70) REVERT: A 67 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7020 (p0) REVERT: A 87 ILE cc_start: 0.9277 (tp) cc_final: 0.8997 (pp) REVERT: A 101 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7654 (mm-40) REVERT: A 116 VAL cc_start: 0.8169 (m) cc_final: 0.7834 (p) REVERT: A 284 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 326 TYR cc_start: 0.9112 (p90) cc_final: 0.8685 (p90) REVERT: A 349 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 416 LEU cc_start: 0.9208 (mt) cc_final: 0.8707 (tt) REVERT: A 427 MET cc_start: 0.7717 (mpp) cc_final: 0.7371 (mpp) REVERT: A 561 ASP cc_start: 0.8038 (t0) cc_final: 0.7774 (t0) REVERT: A 621 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8216 (ttp-110) REVERT: A 798 PHE cc_start: 0.8341 (t80) cc_final: 0.8120 (t80) REVERT: A 831 ASN cc_start: 0.8385 (m-40) cc_final: 0.8029 (m-40) REVERT: A 969 ASP cc_start: 0.8548 (t70) cc_final: 0.8267 (t0) REVERT: B 67 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7060 (p0) REVERT: B 87 ILE cc_start: 0.9347 (tp) cc_final: 0.9020 (pp) REVERT: B 101 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7678 (mm-40) REVERT: B 116 VAL cc_start: 0.8157 (m) cc_final: 0.7895 (p) REVERT: B 143 PHE cc_start: 0.8574 (t80) cc_final: 0.8326 (t80) REVERT: B 326 TYR cc_start: 0.9185 (p90) cc_final: 0.8921 (p90) REVERT: B 349 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7402 (p90) REVERT: B 416 LEU cc_start: 0.9187 (mt) cc_final: 0.8657 (tt) REVERT: B 427 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: B 561 ASP cc_start: 0.8121 (t0) cc_final: 0.7857 (t0) REVERT: B 831 ASN cc_start: 0.8406 (m-40) cc_final: 0.8107 (m-40) REVERT: B 969 ASP cc_start: 0.8639 (t70) cc_final: 0.8318 (t0) REVERT: B 980 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: C 41 ASP cc_start: 0.8849 (t0) cc_final: 0.8605 (t70) REVERT: C 101 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7695 (mm-40) REVERT: C 116 VAL cc_start: 0.8132 (m) cc_final: 0.7765 (p) REVERT: C 326 TYR cc_start: 0.9137 (p90) cc_final: 0.8795 (p90) REVERT: C 349 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6804 (p90) REVERT: C 416 LEU cc_start: 0.9189 (mt) cc_final: 0.8666 (tt) REVERT: C 427 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7405 (mpp) REVERT: C 621 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8141 (ttp-110) REVERT: C 798 PHE cc_start: 0.8403 (t80) cc_final: 0.8090 (m-80) REVERT: C 831 ASN cc_start: 0.8444 (m-40) cc_final: 0.8112 (m-40) REVERT: C 969 ASP cc_start: 0.8571 (t70) cc_final: 0.8309 (t0) outliers start: 49 outliers final: 23 residues processed: 217 average time/residue: 0.9877 time to fit residues: 261.2139 Evaluate side-chains 202 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 915 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 0.0770 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS C 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25374 Z= 0.169 Angle : 0.501 9.227 34521 Z= 0.252 Chirality : 0.043 0.177 4080 Planarity : 0.003 0.070 4380 Dihedral : 4.283 46.550 4496 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.87 % Allowed : 9.55 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3036 helix: 2.11 (0.20), residues: 702 sheet: 0.54 (0.19), residues: 690 loop : -0.54 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 52 HIS 0.002 0.000 HIS C 600 PHE 0.033 0.001 PHE B 346 TYR 0.016 0.001 TYR A1042 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 180 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8823 (t0) cc_final: 0.8525 (t70) REVERT: A 67 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7010 (p0) REVERT: A 87 ILE cc_start: 0.9234 (tp) cc_final: 0.8994 (pp) REVERT: A 101 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7656 (mm-40) REVERT: A 116 VAL cc_start: 0.8191 (m) cc_final: 0.7885 (p) REVERT: A 284 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 326 TYR cc_start: 0.9095 (p90) cc_final: 0.8650 (p90) REVERT: A 349 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6612 (p90) REVERT: A 416 LEU cc_start: 0.9216 (mt) cc_final: 0.8720 (tt) REVERT: A 427 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7294 (mpp) REVERT: A 561 ASP cc_start: 0.8067 (t0) cc_final: 0.7814 (t0) REVERT: A 621 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8219 (ttp-110) REVERT: A 798 PHE cc_start: 0.8330 (t80) cc_final: 0.8111 (t80) REVERT: A 831 ASN cc_start: 0.8368 (m-40) cc_final: 0.8052 (m-40) REVERT: A 969 ASP cc_start: 0.8521 (t70) cc_final: 0.8244 (t0) REVERT: B 67 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7071 (p0) REVERT: B 87 ILE cc_start: 0.9348 (tp) cc_final: 0.9022 (pp) REVERT: B 101 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7680 (mm-40) REVERT: B 116 VAL cc_start: 0.8187 (m) cc_final: 0.7949 (p) REVERT: B 143 PHE cc_start: 0.8557 (t80) cc_final: 0.8248 (t80) REVERT: B 326 TYR cc_start: 0.9147 (p90) cc_final: 0.8762 (p90) REVERT: B 349 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7356 (p90) REVERT: B 416 LEU cc_start: 0.9178 (mt) cc_final: 0.8650 (tt) REVERT: B 427 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7453 (mpp) REVERT: B 561 ASP cc_start: 0.8118 (t0) cc_final: 0.7839 (t0) REVERT: B 831 ASN cc_start: 0.8366 (m-40) cc_final: 0.8073 (m-40) REVERT: B 980 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: C 41 ASP cc_start: 0.8832 (t0) cc_final: 0.8581 (t70) REVERT: C 101 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 116 VAL cc_start: 0.8136 (m) cc_final: 0.7767 (p) REVERT: C 326 TYR cc_start: 0.9133 (p90) cc_final: 0.8787 (p90) REVERT: C 349 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6735 (p90) REVERT: C 416 LEU cc_start: 0.9184 (mt) cc_final: 0.8662 (tt) REVERT: C 427 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7366 (mpp) REVERT: C 621 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8119 (ttp-110) REVERT: C 798 PHE cc_start: 0.8382 (t80) cc_final: 0.8091 (m-80) REVERT: C 831 ASN cc_start: 0.8374 (m-40) cc_final: 0.8084 (m-40) REVERT: C 969 ASP cc_start: 0.8557 (t70) cc_final: 0.8304 (t0) outliers start: 50 outliers final: 24 residues processed: 209 average time/residue: 0.9723 time to fit residues: 248.9134 Evaluate side-chains 209 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 259 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS C 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25374 Z= 0.162 Angle : 0.501 9.841 34521 Z= 0.252 Chirality : 0.043 0.179 4080 Planarity : 0.003 0.070 4380 Dihedral : 4.133 46.707 4496 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.80 % Allowed : 10.07 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3036 helix: 2.14 (0.20), residues: 702 sheet: 0.63 (0.19), residues: 660 loop : -0.50 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 411 HIS 0.003 0.000 HIS B 600 PHE 0.032 0.001 PHE B 346 TYR 0.016 0.001 TYR A1042 ARG 0.002 0.000 ARG C 970 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8799 (t0) cc_final: 0.8479 (t70) REVERT: A 67 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.6963 (p0) REVERT: A 101 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7602 (mm-40) REVERT: A 116 VAL cc_start: 0.8151 (m) cc_final: 0.7838 (p) REVERT: A 284 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 326 TYR cc_start: 0.9094 (p90) cc_final: 0.8643 (p90) REVERT: A 349 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6533 (p90) REVERT: A 416 LEU cc_start: 0.9229 (mt) cc_final: 0.8737 (tt) REVERT: A 427 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: A 621 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8212 (ttp-110) REVERT: A 798 PHE cc_start: 0.8328 (t80) cc_final: 0.8007 (m-80) REVERT: A 831 ASN cc_start: 0.8326 (m-40) cc_final: 0.8015 (m-40) REVERT: A 969 ASP cc_start: 0.8498 (t70) cc_final: 0.8275 (t0) REVERT: B 67 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 87 ILE cc_start: 0.9309 (tp) cc_final: 0.9019 (pp) REVERT: B 101 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7710 (mm-40) REVERT: B 116 VAL cc_start: 0.8223 (m) cc_final: 0.7985 (p) REVERT: B 143 PHE cc_start: 0.8560 (t80) cc_final: 0.8337 (t80) REVERT: B 326 TYR cc_start: 0.9160 (p90) cc_final: 0.8673 (p90) REVERT: B 349 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7331 (p90) REVERT: B 416 LEU cc_start: 0.9197 (mt) cc_final: 0.8684 (tt) REVERT: B 427 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7334 (mpp) REVERT: B 561 ASP cc_start: 0.8130 (t0) cc_final: 0.7828 (t0) REVERT: B 831 ASN cc_start: 0.8312 (m-40) cc_final: 0.8031 (m-40) REVERT: B 980 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: C 41 ASP cc_start: 0.8815 (t0) cc_final: 0.8581 (t70) REVERT: C 101 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7736 (mm-40) REVERT: C 116 VAL cc_start: 0.8132 (m) cc_final: 0.7769 (p) REVERT: C 326 TYR cc_start: 0.9142 (p90) cc_final: 0.8830 (p90) REVERT: C 349 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6721 (p90) REVERT: C 416 LEU cc_start: 0.9174 (mt) cc_final: 0.8666 (tt) REVERT: C 427 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7417 (mpp) REVERT: C 621 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8118 (ttp-110) REVERT: C 798 PHE cc_start: 0.8373 (t80) cc_final: 0.8094 (m-80) REVERT: C 831 ASN cc_start: 0.8319 (m-40) cc_final: 0.8038 (m-40) REVERT: C 969 ASP cc_start: 0.8549 (t70) cc_final: 0.8303 (t0) outliers start: 48 outliers final: 22 residues processed: 215 average time/residue: 0.9423 time to fit residues: 247.1547 Evaluate side-chains 208 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25374 Z= 0.246 Angle : 0.529 9.576 34521 Z= 0.264 Chirality : 0.043 0.189 4080 Planarity : 0.004 0.070 4380 Dihedral : 4.207 48.061 4496 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.54 % Allowed : 10.37 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.15), residues: 3036 helix: 2.06 (0.20), residues: 702 sheet: 0.50 (0.19), residues: 690 loop : -0.53 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 411 HIS 0.003 0.000 HIS B 600 PHE 0.031 0.001 PHE B 346 TYR 0.018 0.001 TYR A 879 ARG 0.002 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8824 (t0) cc_final: 0.8502 (t70) REVERT: A 67 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.6983 (p0) REVERT: A 101 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7658 (mm-40) REVERT: A 116 VAL cc_start: 0.8178 (m) cc_final: 0.7872 (p) REVERT: A 284 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8234 (mm-30) REVERT: A 326 TYR cc_start: 0.9099 (p90) cc_final: 0.8658 (p90) REVERT: A 349 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.6615 (p90) REVERT: A 416 LEU cc_start: 0.9249 (mt) cc_final: 0.8758 (tt) REVERT: A 427 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7260 (mpp) REVERT: A 621 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8222 (ttp-110) REVERT: A 798 PHE cc_start: 0.8346 (t80) cc_final: 0.8117 (t80) REVERT: A 831 ASN cc_start: 0.8385 (m-40) cc_final: 0.8073 (m-40) REVERT: A 969 ASP cc_start: 0.8543 (t70) cc_final: 0.8309 (t0) REVERT: B 67 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7107 (p0) REVERT: B 87 ILE cc_start: 0.9312 (tp) cc_final: 0.9023 (pp) REVERT: B 101 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7695 (mm-40) REVERT: B 116 VAL cc_start: 0.8242 (m) cc_final: 0.7992 (p) REVERT: B 326 TYR cc_start: 0.9153 (p90) cc_final: 0.8665 (p90) REVERT: B 349 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7143 (p90) REVERT: B 416 LEU cc_start: 0.9195 (mt) cc_final: 0.8686 (tt) REVERT: B 427 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7375 (mpp) REVERT: B 561 ASP cc_start: 0.8128 (t0) cc_final: 0.7827 (t0) REVERT: B 831 ASN cc_start: 0.8357 (m-40) cc_final: 0.8096 (m-40) REVERT: B 980 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8612 (mt0) REVERT: C 41 ASP cc_start: 0.8837 (t0) cc_final: 0.8582 (t70) REVERT: C 101 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 116 VAL cc_start: 0.8166 (m) cc_final: 0.7790 (p) REVERT: C 326 TYR cc_start: 0.9130 (p90) cc_final: 0.8692 (p90) REVERT: C 349 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6749 (p90) REVERT: C 416 LEU cc_start: 0.9185 (mt) cc_final: 0.8682 (tt) REVERT: C 427 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7388 (mpp) REVERT: C 621 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8129 (ttp-110) REVERT: C 798 PHE cc_start: 0.8400 (t80) cc_final: 0.8088 (m-80) REVERT: C 831 ASN cc_start: 0.8359 (m-40) cc_final: 0.8013 (m-40) REVERT: C 969 ASP cc_start: 0.8571 (t70) cc_final: 0.8311 (t0) outliers start: 41 outliers final: 22 residues processed: 199 average time/residue: 1.0024 time to fit residues: 243.4331 Evaluate side-chains 200 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 7.9990 chunk 74 optimal weight: 0.0980 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 243 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.115877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071827 restraints weight = 46395.380| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.84 r_work: 0.2829 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25374 Z= 0.171 Angle : 0.518 10.972 34521 Z= 0.257 Chirality : 0.043 0.180 4080 Planarity : 0.003 0.070 4380 Dihedral : 4.101 47.993 4496 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.39 % Allowed : 10.82 % Favored : 87.79 % 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: 0.53 (0.15), residues: 3036 helix: 2.13 (0.20), residues: 702 sheet: 0.52 (0.19), residues: 690 loop : -0.50 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 411 HIS 0.002 0.000 HIS B 600 PHE 0.032 0.001 PHE C 346 TYR 0.016 0.001 TYR A1042 ARG 0.002 0.000 ARG C 970 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.81 seconds wall clock time: 116 minutes 15.33 seconds (6975.33 seconds total)