Starting phenix.real_space_refine on Mon Nov 18 13:27:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psd_17850/11_2024/8psd_17850_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 106 5.16 5 C 15691 2.51 5 N 4032 2.21 5 O 4740 1.98 5 H 23498 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.94s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 48067 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 15987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 15987 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "A" Number of atoms: 15865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 15865 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 9 Chain: "B" Number of atoms: 15711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 15711 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 52, 'TRANS': 964} Chain breaks: 8 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 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 21.95, per 1000 atoms: 0.46 Number of scatterers: 48067 At special positions: 0 Unit cell: (129.346, 135.687, 180.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 O 4740 8.00 N 4032 7.00 C 15691 6.00 H 23498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.04 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " 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 NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 339 " " NAG A1303 " - " ASN A 705 " " NAG A1304 " - " ASN A 713 " " NAG A1305 " - " ASN A 797 " " NAG A1306 " - " ASN A1130 " " NAG A1307 " - " ASN A 612 " " NAG A1309 " - " ASN A1094 " " NAG A1310 " - " ASN A 278 " " NAG A1311 " - " ASN A 327 " " NAG B1301 " - " ASN B 58 " " NAG B1303 " - " ASN B 339 " " NAG B1304 " - " ASN B 705 " " NAG B1305 " - " ASN B 713 " " NAG B1306 " - " ASN B 797 " " NAG B1307 " - " ASN B1130 " " NAG B1308 " - " ASN B 612 " " NAG B1309 " - " ASN B1094 " " NAG B1310 " - " ASN B 278 " " NAG B1312 " - " ASN B1070 " " NAG C1301 " - " ASN C 58 " " NAG C1303 " - " ASN C 339 " " NAG C1304 " - " ASN C 705 " " NAG C1305 " - " ASN C 713 " " NAG C1306 " - " ASN C 797 " " NAG C1307 " - " ASN C1130 " " NAG C1308 " - " ASN C 612 " " NAG C1310 " - " ASN C1094 " " NAG C1311 " - " ASN C 278 " " NAG C1312 " - " ASN C 327 " Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 3.7 seconds 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5782 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 44 sheets defined 26.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 334 through 339 removed outlier: 3.521A pdb=" N PHE C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.646A pdb=" N VAL C 363 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.707A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.375A pdb=" N SER C 404 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.656A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.511A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 852 removed outlier: 3.610A pdb=" N ASN C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 885 Processing helix chain 'C' and resid 893 through 904 Processing helix chain 'C' and resid 908 through 914 removed outlier: 4.207A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.977A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 3.848A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C1013 " --> pdb=" O ILE C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1142 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.518A pdb=" N PHE A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.970A pdb=" N ASN A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.505A pdb=" N SER A 404 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 406 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.518A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.594A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 886 " --> pdb=" O THR A 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 886' Processing helix chain 'A' and resid 893 through 904 Processing helix chain 'A' and resid 908 through 914 removed outlier: 4.113A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 Processing helix chain 'A' and resid 944 through 961 removed outlier: 4.035A pdb=" N VAL A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 3.978A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1029 " --> pdb=" O MET A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1142 removed outlier: 4.499A pdb=" N ASP A1142 " --> pdb=" O GLN A1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 360 through 367 removed outlier: 3.885A pdb=" N TYR B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.038A pdb=" N LEU B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 385 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.297A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.810A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.599A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.611A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.907A pdb=" N GLY B 887 " --> pdb=" O PHE B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 904 Processing helix chain 'B' and resid 908 through 914 removed outlier: 4.010A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.823A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 3.969A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B1013 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B1029 " --> pdb=" O MET B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1142 removed outlier: 4.145A pdb=" N ASP B1142 " --> pdb=" O GLN B1138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 28 removed outlier: 7.986A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 91 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 186 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 223 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 201 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 52 removed outlier: 4.094A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'C' and resid 307 through 315 removed outlier: 5.434A pdb=" N ILE C 308 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 595 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLN C 310 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 593 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 312 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AA6, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.722A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AA8, first strand: chain 'C' and resid 535 through 539 removed outlier: 5.697A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 650 through 651 removed outlier: 5.989A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB2, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.769A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.769A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C1072 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.741A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 784 through 786 removed outlier: 5.924A pdb=" N ILE C 784 " --> pdb=" O ASN B 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AB7, first strand: chain 'A' and resid 20 through 27 removed outlier: 7.778A pdb=" N ASN A 58 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 265 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 223 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 44 through 52 removed outlier: 7.720A pdb=" N THR A 270 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP A 286 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 272 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 284 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 274 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AC1, first strand: chain 'A' and resid 307 through 315 removed outlier: 7.042A pdb=" N VAL A 591 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 313 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY A 589 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.754A pdb=" N ALA A 571 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE A 561 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AC4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.740A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AC6, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.070A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 698 through 700 Processing sheet with id=AC8, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.763A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 716 " --> pdb=" O TYR A1063 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A1063 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 718 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1061 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 720 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A1059 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 722 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1057 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A1055 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.763A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 716 " --> pdb=" O TYR A1063 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A1063 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 718 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1061 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 720 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A1059 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 722 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1057 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A1055 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.653A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AD3, first strand: chain 'B' and resid 20 through 27 removed outlier: 8.467A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 223 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 44 through 52 removed outlier: 4.104A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AD6, first strand: chain 'B' and resid 307 through 315 removed outlier: 5.686A pdb=" N ILE B 308 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 595 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 310 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 593 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 312 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 350 through 354 Processing sheet with id=AD8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.653A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AE1, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AE2, first strand: chain 'B' and resid 535 through 539 removed outlier: 5.706A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 571 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 650 through 651 removed outlier: 5.971A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 708 through 710 Processing sheet with id=AE5, first strand: chain 'B' and resid 713 through 724 removed outlier: 6.033A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.622A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AE8, first strand: chain 'B' and resid 1090 through 1093 995 hydrogen bonds defined for protein. 2652 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: 20.46 Time building geometry restraints manager: 13.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23478 1.03 - 1.23: 412 1.23 - 1.43: 10259 1.43 - 1.62: 14344 1.62 - 1.82: 130 Bond restraints: 48623 Sorted by residual: bond pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 48618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 81806 1.02 - 2.05: 5164 2.05 - 3.07: 301 3.07 - 4.10: 108 4.10 - 5.12: 13 Bond angle restraints: 87392 Sorted by residual: angle pdb=" N LEU C 222 " pdb=" CA LEU C 222 " pdb=" C LEU C 222 " ideal model delta sigma weight residual 111.04 115.50 -4.46 1.55e+00 4.16e-01 8.29e+00 angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 111.04 115.13 -4.09 1.55e+00 4.16e-01 6.98e+00 angle pdb=" N LEU B 222 " pdb=" CA LEU B 222 " pdb=" C LEU B 222 " ideal model delta sigma weight residual 111.02 114.99 -3.97 1.52e+00 4.33e-01 6.81e+00 angle pdb=" N PRO C 221 " pdb=" CA PRO C 221 " pdb=" C PRO C 221 " ideal model delta sigma weight residual 112.47 117.48 -5.01 2.06e+00 2.36e-01 5.92e+00 angle pdb=" N PRO A 221 " pdb=" CA PRO A 221 " pdb=" C PRO A 221 " ideal model delta sigma weight residual 112.47 117.41 -4.94 2.06e+00 2.36e-01 5.74e+00 ... (remaining 87387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 23005 25.20 - 50.40: 679 50.40 - 75.60: 166 75.60 - 100.81: 5 100.81 - 126.01: 20 Dihedral angle restraints: 23875 sinusoidal: 13084 harmonic: 10791 Sorted by residual: dihedral pdb=" C2 NAG B1302 " pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " pdb=" C5 NAG B1302 " ideal model delta sinusoidal sigma weight residual -62.96 63.05 -126.01 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C2 NAG C1312 " pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " pdb=" C5 NAG C1312 " ideal model delta sinusoidal sigma weight residual -62.96 52.37 -115.33 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C1 NAG C1312 " pdb=" C5 NAG C1312 " pdb=" O5 NAG C1312 " pdb=" C4 NAG C1312 " ideal model delta sinusoidal sigma weight residual -64.11 49.72 -113.83 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 23872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3421 0.060 - 0.120: 506 0.120 - 0.179: 65 0.179 - 0.239: 2 0.239 - 0.299: 1 Chirality restraints: 3995 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 327 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C1130 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 339 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 3992 not shown) Planarity restraints: 7283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 185 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C LEU C 185 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU C 185 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG C 186 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 848 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ALA A 848 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 848 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 849 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1048 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A1049 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1049 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1049 " 0.020 5.00e-02 4.00e+02 ... (remaining 7280 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1623 2.19 - 2.79: 92918 2.79 - 3.39: 118738 3.39 - 4.00: 161527 4.00 - 4.60: 251121 Nonbonded interactions: 625927 Sorted by model distance: nonbonded pdb=" HG1 THR C 712 " pdb=" O GLN C1067 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASN B 119 " pdb=" H ALA B 120 " model vdw 1.629 2.450 nonbonded pdb=" HG1 THR A 712 " pdb=" O GLN A1067 " model vdw 1.636 2.450 nonbonded pdb=" O ALA C 875 " pdb=" HG1 THR C 879 " model vdw 1.636 2.450 nonbonded pdb=" O THR A 389 " pdb=" HG1 THR A 519 " model vdw 1.639 2.450 ... (remaining 625922 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' and (resid 19 through 65 or resid 78 through 92 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or n \ ame HG23 or name HD11 or name HD12 or name HD13)) or resid 98 through 138 or (re \ sid 163 and (name N or name CA or name C or name O or name CB or name OG1 or nam \ e CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG23)) \ or resid 164 through 167 or (resid 185 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name \ HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 \ or name HD23)) or resid 186 through 204 or resid 212 through 225 or (resid 226 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me HA )) or resid 227 through 470 or (resid 483 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 484 through 1069 or (resid 1070 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or resid 1 \ 071 through 1142 or resid 1301 through 1311)) selection = (chain 'B' and (resid 19 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 129 through 167 or resid 185 through 225 or (resid 226 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name HA )) or \ resid 227 through 470 or (resid 483 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 \ or name HD21 or name HD22)) or resid 484 through 619 or (resid 623 and (name N o \ r name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or n \ ame HA or name HB2 or name HB3)) or resid 624 through 633 or (resid 638 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA \ or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or \ name HG23)) or resid 639 through 832 or resid 844 through 1142 or resid 1301 thr \ ough 1311)) selection = (chain 'C' and (resid 19 through 65 or (resid 78 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 79 through 92 or (resid 97 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 \ or name HG23 or name HD11 or name HD12 or name HD13)) or resid 98 through 127 o \ r (resid 128 and (name N or name CA or name C or name O or name CB or name SG or \ name H or name HA or name HB2 or name HB3)) or resid 129 through 138 or (resid \ 163 and (name N or name CA or name C or name O or name CB or name OG1 or name CG \ 2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG23)) or \ resid 164 through 167 or (resid 185 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 \ or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or n \ ame HD23)) or resid 186 through 204 or (resid 212 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 213 through 619 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 633 or (resid 638 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or \ name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or nam \ e HG23)) or resid 639 through 832 or resid 844 through 1069 or (resid 1070 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or resid 1071 th \ rough 1142 or resid 1301 through 1311)) } 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: 2.180 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: 0.810 Extract box with map and model: 1.640 Check model and map are aligned: 0.320 Set scattering table: 0.430 Process input model: 94.290 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.140 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:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 0.054 25125 Z= 0.243 Angle : 0.506 5.124 34188 Z= 0.258 Chirality : 0.045 0.299 3995 Planarity : 0.003 0.036 4361 Dihedral : 12.295 126.008 9548 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.60 % Allowed : 4.95 % Favored : 93.45 % 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: -0.16 (0.15), residues: 3022 helix: 1.87 (0.21), residues: 715 sheet: 0.79 (0.19), residues: 674 loop : -1.49 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 882 HIS 0.004 0.001 HIS B1060 PHE 0.011 0.001 PHE C1117 TYR 0.014 0.001 TYR B1063 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 334 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8644 (p) cc_final: 0.8404 (m) REVERT: C 110 LYS cc_start: 0.6959 (mptt) cc_final: 0.6363 (tptp) REVERT: C 454 LYS cc_start: 0.8531 (tptp) cc_final: 0.8290 (mppt) REVERT: C 599 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8429 (t0) REVERT: C 693 MET cc_start: 0.9228 (ptt) cc_final: 0.9008 (ptp) REVERT: C 960 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8250 (ttpp) REVERT: C 998 GLN cc_start: 0.8266 (tt0) cc_final: 0.7996 (tp40) REVERT: A 112 GLN cc_start: 0.6274 (mt0) cc_final: 0.6056 (mt0) REVERT: A 185 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6941 (mt) REVERT: A 305 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7665 (mp0) REVERT: A 310 GLN cc_start: 0.8114 (tt0) cc_final: 0.7793 (pt0) REVERT: A 374 LYS cc_start: 0.8009 (tppp) cc_final: 0.7268 (tmtt) REVERT: A 454 LYS cc_start: 0.8421 (mtpm) cc_final: 0.7689 (pmtt) REVERT: A 525 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7305 (tptp) REVERT: A 790 ILE cc_start: 0.8191 (mt) cc_final: 0.7714 (pp) REVERT: A 898 MET cc_start: 0.9034 (mmt) cc_final: 0.8787 (mmt) REVERT: A 1034 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8498 (mmtp) REVERT: A 1114 ASP cc_start: 0.7657 (m-30) cc_final: 0.7411 (m-30) REVERT: A 1118 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 1134 TYR cc_start: 0.8241 (t80) cc_final: 0.7885 (t80) REVERT: B 98 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6254 (pp) REVERT: B 99 ARG cc_start: 0.6029 (mmm-85) cc_final: 0.5296 (mpt180) REVERT: B 186 ARG cc_start: 0.6285 (mtt-85) cc_final: 0.5474 (mpp-170) REVERT: B 222 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7307 (mm) REVERT: B 294 GLU cc_start: 0.8088 (tt0) cc_final: 0.7719 (tt0) REVERT: B 315 ARG cc_start: 0.7508 (ptp90) cc_final: 0.6805 (ptm160) REVERT: B 362 SER cc_start: 0.9243 (t) cc_final: 0.8923 (p) REVERT: B 374 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7190 (tptt) REVERT: B 410 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: B 525 LYS cc_start: 0.8006 (mtpm) cc_final: 0.7743 (tttp) REVERT: B 533 LYS cc_start: 0.8139 (mttm) cc_final: 0.7759 (mtmt) REVERT: B 561 PHE cc_start: 0.7827 (p90) cc_final: 0.7409 (p90) REVERT: B 624 GLN cc_start: 0.7004 (mt0) cc_final: 0.6770 (mt0) REVERT: B 671 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7268 (mp10) REVERT: B 960 LYS cc_start: 0.8271 (tttt) cc_final: 0.7997 (mtmt) outliers start: 43 outliers final: 11 residues processed: 368 average time/residue: 2.5472 time to fit residues: 1100.8811 Evaluate side-chains 224 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9980 chunk 231 optimal weight: 0.0000 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.0010 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 GLN B 27 ASN B1050 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25125 Z= 0.174 Angle : 0.492 8.760 34188 Z= 0.257 Chirality : 0.044 0.203 3995 Planarity : 0.004 0.034 4361 Dihedral : 9.372 91.546 4079 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.64 % Allowed : 10.16 % Favored : 88.20 % 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: -0.21 (0.15), residues: 3022 helix: 1.87 (0.21), residues: 714 sheet: 0.73 (0.19), residues: 682 loop : -1.54 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 432 HIS 0.003 0.001 HIS B1060 PHE 0.011 0.001 PHE A 62 TYR 0.014 0.001 TYR B1063 ARG 0.003 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8667 (p) cc_final: 0.8436 (m) REVERT: C 110 LYS cc_start: 0.6961 (mptt) cc_final: 0.6320 (tptp) REVERT: C 317 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8306 (mm-40) REVERT: C 454 LYS cc_start: 0.8512 (tptp) cc_final: 0.8286 (mppt) REVERT: C 693 MET cc_start: 0.9219 (ptt) cc_final: 0.8998 (ptp) REVERT: C 960 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8263 (ttpp) REVERT: C 998 GLN cc_start: 0.8251 (tt0) cc_final: 0.8013 (tp40) REVERT: A 185 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6951 (mt) REVERT: A 233 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7606 (mtm-85) REVERT: A 274 LYS cc_start: 0.8031 (tttm) cc_final: 0.7745 (ttpt) REVERT: A 305 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7430 (mp0) REVERT: A 310 GLN cc_start: 0.8101 (tt0) cc_final: 0.7843 (pt0) REVERT: A 374 LYS cc_start: 0.8009 (tppp) cc_final: 0.7266 (tmtt) REVERT: A 454 LYS cc_start: 0.8398 (mtpm) cc_final: 0.7651 (pmtt) REVERT: A 520 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7173 (p) REVERT: A 525 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7313 (tptp) REVERT: A 790 ILE cc_start: 0.8191 (mt) cc_final: 0.7715 (pp) REVERT: A 1034 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8387 (mmtp) REVERT: A 1114 ASP cc_start: 0.7812 (m-30) cc_final: 0.7568 (m-30) REVERT: A 1118 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8713 (p) REVERT: A 1134 TYR cc_start: 0.8241 (t80) cc_final: 0.7893 (t80) REVERT: B 99 ARG cc_start: 0.6042 (mmm-85) cc_final: 0.5274 (mpt180) REVERT: B 165 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6356 (mm-30) REVERT: B 186 ARG cc_start: 0.6293 (mtt-85) cc_final: 0.5513 (mmp80) REVERT: B 294 GLU cc_start: 0.8052 (tt0) cc_final: 0.7525 (tt0) REVERT: B 315 ARG cc_start: 0.7375 (ptp90) cc_final: 0.6730 (ptm160) REVERT: B 362 SER cc_start: 0.9174 (t) cc_final: 0.8963 (p) REVERT: B 374 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7268 (tptt) REVERT: B 410 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: B 467 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6629 (mt-10) REVERT: B 525 LYS cc_start: 0.8135 (mtpm) cc_final: 0.7899 (tttp) REVERT: B 533 LYS cc_start: 0.8112 (mttm) cc_final: 0.7757 (mtmt) REVERT: B 561 PHE cc_start: 0.7830 (p90) cc_final: 0.7396 (p90) REVERT: B 588 PHE cc_start: 0.8234 (p90) cc_final: 0.8006 (p90) REVERT: B 624 GLN cc_start: 0.6976 (mt0) cc_final: 0.6774 (mt0) REVERT: B 671 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7230 (mp10) REVERT: B 960 LYS cc_start: 0.8263 (tttt) cc_final: 0.8014 (mtmt) outliers start: 44 outliers final: 23 residues processed: 253 average time/residue: 2.6141 time to fit residues: 776.9109 Evaluate side-chains 236 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 300 optimal weight: 0.0870 chunk 247 optimal weight: 0.0270 chunk 276 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN A 953 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25125 Z= 0.170 Angle : 0.476 7.501 34188 Z= 0.248 Chirality : 0.044 0.272 3995 Planarity : 0.004 0.033 4361 Dihedral : 7.908 59.390 4073 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.82 % Allowed : 10.20 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3022 helix: 1.88 (0.20), residues: 714 sheet: 0.73 (0.19), residues: 676 loop : -1.53 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 432 HIS 0.003 0.001 HIS B1060 PHE 0.011 0.001 PHE A1117 TYR 0.014 0.001 TYR B1063 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8659 (p) cc_final: 0.8428 (m) REVERT: C 110 LYS cc_start: 0.6944 (mptt) cc_final: 0.6311 (tptp) REVERT: C 184 ASN cc_start: 0.6789 (m-40) cc_final: 0.5926 (p0) REVERT: C 317 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8304 (mm-40) REVERT: C 454 LYS cc_start: 0.8506 (tptp) cc_final: 0.8284 (mppt) REVERT: C 693 MET cc_start: 0.9219 (ptt) cc_final: 0.8999 (ptp) REVERT: C 998 GLN cc_start: 0.8253 (tt0) cc_final: 0.8012 (tp40) REVERT: A 185 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6947 (mt) REVERT: A 274 LYS cc_start: 0.8031 (tttm) cc_final: 0.7734 (ttpt) REVERT: A 305 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7525 (mp0) REVERT: A 310 GLN cc_start: 0.8053 (tt0) cc_final: 0.7783 (pt0) REVERT: A 374 LYS cc_start: 0.8004 (tppp) cc_final: 0.7263 (tmtt) REVERT: A 454 LYS cc_start: 0.8466 (mtpm) cc_final: 0.7677 (pmtt) REVERT: A 520 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7204 (p) REVERT: A 525 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7414 (mmtm) REVERT: A 790 ILE cc_start: 0.8195 (mt) cc_final: 0.7716 (pp) REVERT: A 1034 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8392 (mmtp) REVERT: A 1114 ASP cc_start: 0.7799 (m-30) cc_final: 0.7568 (m-30) REVERT: A 1118 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8732 (p) REVERT: A 1134 TYR cc_start: 0.8230 (t80) cc_final: 0.7894 (t80) REVERT: B 99 ARG cc_start: 0.6023 (mmm-85) cc_final: 0.5319 (mpt180) REVERT: B 165 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6389 (mm-30) REVERT: B 186 ARG cc_start: 0.6347 (mtt-85) cc_final: 0.5470 (mmp80) REVERT: B 294 GLU cc_start: 0.8088 (tt0) cc_final: 0.7644 (tt0) REVERT: B 315 ARG cc_start: 0.7446 (ptp90) cc_final: 0.6761 (ptm160) REVERT: B 362 SER cc_start: 0.9156 (t) cc_final: 0.8928 (p) REVERT: B 374 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7275 (tptt) REVERT: B 410 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: B 467 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6571 (mt-10) REVERT: B 525 LYS cc_start: 0.8155 (mtpm) cc_final: 0.7912 (tttp) REVERT: B 533 LYS cc_start: 0.8120 (mttm) cc_final: 0.7765 (mtmt) REVERT: B 561 PHE cc_start: 0.7944 (p90) cc_final: 0.7534 (p90) REVERT: B 671 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7243 (mp10) REVERT: B 960 LYS cc_start: 0.8258 (tttt) cc_final: 0.8013 (mtmt) REVERT: B 1046 MET cc_start: 0.8213 (mtp) cc_final: 0.7869 (mtp) outliers start: 49 outliers final: 23 residues processed: 251 average time/residue: 2.5626 time to fit residues: 761.1325 Evaluate side-chains 230 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN A 953 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25125 Z= 0.206 Angle : 0.483 6.357 34188 Z= 0.253 Chirality : 0.044 0.225 3995 Planarity : 0.004 0.034 4361 Dihedral : 7.418 59.342 4073 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.94 % Allowed : 10.83 % Favored : 87.23 % 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: -0.25 (0.15), residues: 3022 helix: 1.84 (0.20), residues: 714 sheet: 0.74 (0.19), residues: 673 loop : -1.57 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 432 HIS 0.004 0.001 HIS B1060 PHE 0.012 0.001 PHE A1117 TYR 0.014 0.001 TYR B1063 ARG 0.003 0.000 ARG A1103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8673 (p) cc_final: 0.8429 (m) REVERT: C 110 LYS cc_start: 0.6921 (mptt) cc_final: 0.6292 (tptp) REVERT: C 192 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5840 (t0) REVERT: C 317 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8324 (mm-40) REVERT: C 454 LYS cc_start: 0.8512 (tptp) cc_final: 0.8291 (mppt) REVERT: C 693 MET cc_start: 0.9233 (ptt) cc_final: 0.9011 (ptp) REVERT: C 998 GLN cc_start: 0.8275 (tt0) cc_final: 0.8054 (tp40) REVERT: A 185 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6946 (mt) REVERT: A 216 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 274 LYS cc_start: 0.8034 (tttm) cc_final: 0.7713 (ttpt) REVERT: A 283 ASP cc_start: 0.8107 (t0) cc_final: 0.7891 (t0) REVERT: A 305 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7509 (mp0) REVERT: A 310 GLN cc_start: 0.8009 (tt0) cc_final: 0.7802 (pt0) REVERT: A 374 LYS cc_start: 0.8030 (tppp) cc_final: 0.7128 (tptt) REVERT: A 454 LYS cc_start: 0.8481 (mtpm) cc_final: 0.7688 (pmtt) REVERT: A 520 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7253 (p) REVERT: A 525 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7423 (mmtm) REVERT: A 561 PHE cc_start: 0.7783 (m-10) cc_final: 0.7580 (m-80) REVERT: A 790 ILE cc_start: 0.8202 (mt) cc_final: 0.7735 (pp) REVERT: A 1034 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8399 (mmtp) REVERT: A 1114 ASP cc_start: 0.7868 (m-30) cc_final: 0.7642 (m-30) REVERT: A 1118 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8754 (p) REVERT: A 1134 TYR cc_start: 0.8238 (t80) cc_final: 0.7928 (t80) REVERT: B 99 ARG cc_start: 0.6039 (mmm-85) cc_final: 0.5331 (mpt180) REVERT: B 165 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6382 (mm-30) REVERT: B 186 ARG cc_start: 0.6340 (mtt-85) cc_final: 0.5413 (mmp80) REVERT: B 294 GLU cc_start: 0.8098 (tt0) cc_final: 0.7647 (tt0) REVERT: B 315 ARG cc_start: 0.7458 (ptp90) cc_final: 0.6761 (ptm160) REVERT: B 362 SER cc_start: 0.9146 (t) cc_final: 0.8877 (m) REVERT: B 374 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7225 (tptt) REVERT: B 410 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: B 525 LYS cc_start: 0.8166 (mtpm) cc_final: 0.7918 (tttp) REVERT: B 533 LYS cc_start: 0.8132 (mttm) cc_final: 0.7776 (mtmt) REVERT: B 561 PHE cc_start: 0.7957 (p90) cc_final: 0.7550 (p90) REVERT: B 642 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8069 (mtp180) REVERT: B 671 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7279 (mp10) REVERT: B 960 LYS cc_start: 0.8290 (tttt) cc_final: 0.8040 (mtmt) REVERT: B 1046 MET cc_start: 0.8288 (mtp) cc_final: 0.7889 (mtp) outliers start: 52 outliers final: 27 residues processed: 249 average time/residue: 2.5117 time to fit residues: 741.0522 Evaluate side-chains 231 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN A 953 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25125 Z= 0.176 Angle : 0.475 5.232 34188 Z= 0.249 Chirality : 0.044 0.222 3995 Planarity : 0.004 0.034 4361 Dihedral : 7.118 58.907 4073 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.82 % Allowed : 11.02 % Favored : 87.16 % 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: -0.25 (0.15), residues: 3022 helix: 1.88 (0.20), residues: 714 sheet: 0.73 (0.19), residues: 673 loop : -1.59 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 432 HIS 0.003 0.001 HIS B1060 PHE 0.011 0.001 PHE A1117 TYR 0.014 0.001 TYR B1063 ARG 0.002 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8670 (p) cc_final: 0.8424 (m) REVERT: C 110 LYS cc_start: 0.6909 (mptt) cc_final: 0.6286 (tptp) REVERT: C 184 ASN cc_start: 0.6815 (m-40) cc_final: 0.5959 (p0) REVERT: C 192 ASN cc_start: 0.6417 (OUTLIER) cc_final: 0.5830 (t0) REVERT: C 317 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8337 (mm-40) REVERT: C 454 LYS cc_start: 0.8510 (tptp) cc_final: 0.8289 (mppt) REVERT: C 693 MET cc_start: 0.9232 (ptt) cc_final: 0.9004 (ptp) REVERT: C 998 GLN cc_start: 0.8275 (tt0) cc_final: 0.8073 (tp40) REVERT: A 185 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6941 (mt) REVERT: A 216 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6884 (t80) REVERT: A 274 LYS cc_start: 0.8033 (tttm) cc_final: 0.7777 (ttpt) REVERT: A 283 ASP cc_start: 0.8145 (t0) cc_final: 0.7909 (t0) REVERT: A 305 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7490 (mp0) REVERT: A 374 LYS cc_start: 0.8015 (tppp) cc_final: 0.7272 (tmtt) REVERT: A 454 LYS cc_start: 0.8486 (mtpm) cc_final: 0.7693 (pmtt) REVERT: A 520 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7255 (p) REVERT: A 525 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7438 (mmtm) REVERT: A 550 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: A 561 PHE cc_start: 0.7783 (m-10) cc_final: 0.7580 (m-80) REVERT: A 790 ILE cc_start: 0.8193 (mt) cc_final: 0.7728 (pp) REVERT: A 1034 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8398 (mmtp) REVERT: A 1114 ASP cc_start: 0.7835 (m-30) cc_final: 0.7606 (m-30) REVERT: A 1118 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8736 (p) REVERT: A 1134 TYR cc_start: 0.8239 (t80) cc_final: 0.7883 (t80) REVERT: B 99 ARG cc_start: 0.6152 (mmm-85) cc_final: 0.5448 (mpt180) REVERT: B 165 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6412 (mm-30) REVERT: B 186 ARG cc_start: 0.6346 (mtt-85) cc_final: 0.5409 (mmp80) REVERT: B 219 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7433 (mt) REVERT: B 294 GLU cc_start: 0.8065 (tt0) cc_final: 0.7606 (tt0) REVERT: B 310 GLN cc_start: 0.8350 (tt0) cc_final: 0.8068 (tt0) REVERT: B 315 ARG cc_start: 0.7389 (ptp90) cc_final: 0.6701 (ptm160) REVERT: B 362 SER cc_start: 0.9142 (t) cc_final: 0.8880 (m) REVERT: B 374 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7288 (tptt) REVERT: B 410 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: B 525 LYS cc_start: 0.8158 (mtpm) cc_final: 0.7927 (tttp) REVERT: B 530 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 533 LYS cc_start: 0.8124 (mttm) cc_final: 0.7767 (mtmt) REVERT: B 561 PHE cc_start: 0.7957 (p90) cc_final: 0.7544 (p90) REVERT: B 671 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7272 (mp10) REVERT: B 960 LYS cc_start: 0.8268 (tttt) cc_final: 0.8028 (mtmt) REVERT: B 1046 MET cc_start: 0.8286 (mtp) cc_final: 0.7887 (mtp) outliers start: 49 outliers final: 31 residues processed: 238 average time/residue: 2.6155 time to fit residues: 737.3191 Evaluate side-chains 241 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25125 Z= 0.182 Angle : 0.471 4.508 34188 Z= 0.247 Chirality : 0.044 0.220 3995 Planarity : 0.004 0.035 4361 Dihedral : 6.787 58.795 4072 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.12 % Allowed : 10.79 % Favored : 87.09 % 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: -0.25 (0.15), residues: 3022 helix: 1.90 (0.20), residues: 714 sheet: 0.72 (0.19), residues: 673 loop : -1.60 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 432 HIS 0.003 0.001 HIS B1060 PHE 0.011 0.001 PHE A1117 TYR 0.014 0.001 TYR C1134 ARG 0.003 0.000 ARG A1103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 3.700 Fit side-chains revert: symmetry clash REVERT: C 91 SER cc_start: 0.8673 (p) cc_final: 0.8426 (m) REVERT: C 110 LYS cc_start: 0.6898 (mptt) cc_final: 0.6282 (tptp) REVERT: C 184 ASN cc_start: 0.6861 (m-40) cc_final: 0.6044 (p0) REVERT: C 192 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.5838 (t0) REVERT: C 317 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8349 (mm-40) REVERT: C 454 LYS cc_start: 0.8509 (tptp) cc_final: 0.8282 (mppt) REVERT: C 693 MET cc_start: 0.9194 (ptt) cc_final: 0.8967 (ptp) REVERT: C 998 GLN cc_start: 0.8260 (tt0) cc_final: 0.8043 (tp40) REVERT: A 185 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6948 (mt) REVERT: A 216 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6802 (t80) REVERT: A 283 ASP cc_start: 0.8155 (t0) cc_final: 0.7880 (t0) REVERT: A 305 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7480 (mp0) REVERT: A 374 LYS cc_start: 0.8014 (tppp) cc_final: 0.7272 (tmtt) REVERT: A 454 LYS cc_start: 0.8496 (mtpm) cc_final: 0.7699 (pmtt) REVERT: A 520 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7370 (p) REVERT: A 525 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7439 (mmtm) REVERT: A 550 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: A 790 ILE cc_start: 0.8200 (mt) cc_final: 0.7732 (pp) REVERT: A 1034 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8398 (mmtp) REVERT: A 1114 ASP cc_start: 0.7841 (m-30) cc_final: 0.7610 (m-30) REVERT: A 1118 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 1134 TYR cc_start: 0.8249 (t80) cc_final: 0.7915 (t80) REVERT: B 99 ARG cc_start: 0.6144 (mmm-85) cc_final: 0.5446 (mpt180) REVERT: B 165 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6412 (mm-30) REVERT: B 186 ARG cc_start: 0.6366 (mtt-85) cc_final: 0.5381 (mmp80) REVERT: B 219 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7516 (mt) REVERT: B 294 GLU cc_start: 0.8070 (tt0) cc_final: 0.7603 (tt0) REVERT: B 310 GLN cc_start: 0.8360 (tt0) cc_final: 0.8086 (tt0) REVERT: B 315 ARG cc_start: 0.7398 (ptp90) cc_final: 0.6700 (ptm160) REVERT: B 362 SER cc_start: 0.9136 (t) cc_final: 0.8883 (m) REVERT: B 374 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7291 (tptt) REVERT: B 410 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 525 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7906 (tttp) REVERT: B 530 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 533 LYS cc_start: 0.8128 (mttm) cc_final: 0.7768 (mtmt) REVERT: B 561 PHE cc_start: 0.7935 (p90) cc_final: 0.7509 (p90) REVERT: B 671 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7094 (mp10) REVERT: B 960 LYS cc_start: 0.8270 (tttt) cc_final: 0.8029 (mtmt) REVERT: B 1046 MET cc_start: 0.8291 (mtp) cc_final: 0.7885 (mtp) outliers start: 57 outliers final: 33 residues processed: 238 average time/residue: 2.5615 time to fit residues: 720.9293 Evaluate side-chains 234 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN C 686 GLN A 953 GLN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25125 Z= 0.358 Angle : 0.553 4.993 34188 Z= 0.294 Chirality : 0.047 0.270 3995 Planarity : 0.004 0.038 4361 Dihedral : 7.071 59.382 4072 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.42 % Allowed : 11.09 % Favored : 86.49 % 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: 3022 helix: 1.57 (0.20), residues: 711 sheet: 0.58 (0.19), residues: 684 loop : -1.76 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 349 HIS 0.008 0.001 HIS B1060 PHE 0.019 0.002 PHE A1117 TYR 0.018 0.002 TYR A 491 ARG 0.004 0.001 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 3.688 Fit side-chains revert: symmetry clash REVERT: C 91 SER cc_start: 0.8612 (p) cc_final: 0.8327 (m) REVERT: C 110 LYS cc_start: 0.6825 (mptt) cc_final: 0.6283 (tptp) REVERT: C 192 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.5854 (t0) REVERT: C 317 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8280 (mm-40) REVERT: C 454 LYS cc_start: 0.8526 (tptp) cc_final: 0.8302 (mppt) REVERT: C 693 MET cc_start: 0.9268 (ptt) cc_final: 0.9043 (ptp) REVERT: A 185 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6954 (mt) REVERT: A 216 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6673 (t80) REVERT: A 283 ASP cc_start: 0.8207 (t0) cc_final: 0.7942 (t0) REVERT: A 305 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7434 (mp0) REVERT: A 374 LYS cc_start: 0.8216 (tppp) cc_final: 0.7284 (tptt) REVERT: A 454 LYS cc_start: 0.8472 (mtpm) cc_final: 0.7708 (pmtt) REVERT: A 520 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 525 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7436 (mmtm) REVERT: A 790 ILE cc_start: 0.8230 (mt) cc_final: 0.7763 (pp) REVERT: A 998 GLN cc_start: 0.8273 (tt0) cc_final: 0.8025 (tp40) REVERT: A 1034 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8603 (mmtp) REVERT: A 1114 ASP cc_start: 0.7827 (m-30) cc_final: 0.7590 (m-30) REVERT: A 1118 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 1134 TYR cc_start: 0.8264 (t80) cc_final: 0.7963 (t80) REVERT: B 99 ARG cc_start: 0.6226 (mmm-85) cc_final: 0.5479 (mpt180) REVERT: B 165 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: B 186 ARG cc_start: 0.6295 (mtt-85) cc_final: 0.5327 (mmp80) REVERT: B 294 GLU cc_start: 0.8107 (tt0) cc_final: 0.7646 (tt0) REVERT: B 310 GLN cc_start: 0.8462 (tt0) cc_final: 0.8208 (tt0) REVERT: B 315 ARG cc_start: 0.7421 (ptp90) cc_final: 0.6752 (ptm160) REVERT: B 362 SER cc_start: 0.9140 (t) cc_final: 0.8874 (m) REVERT: B 374 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7313 (tptt) REVERT: B 410 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: B 467 GLU cc_start: 0.6798 (mt-10) cc_final: 0.5844 (pp20) REVERT: B 525 LYS cc_start: 0.8174 (mtpm) cc_final: 0.7926 (tttp) REVERT: B 530 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 533 LYS cc_start: 0.8208 (mttm) cc_final: 0.7842 (mtmt) REVERT: B 561 PHE cc_start: 0.8027 (p90) cc_final: 0.7610 (p90) REVERT: B 671 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7253 (mp10) REVERT: B 960 LYS cc_start: 0.8449 (tttt) cc_final: 0.8221 (mtmt) REVERT: B 998 GLN cc_start: 0.8152 (tp40) cc_final: 0.7931 (mm-40) REVERT: B 1046 MET cc_start: 0.8371 (mtp) cc_final: 0.7963 (mtp) outliers start: 65 outliers final: 43 residues processed: 238 average time/residue: 2.6547 time to fit residues: 748.4033 Evaluate side-chains 235 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN C 998 GLN A 112 GLN A 953 GLN A1121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25125 Z= 0.171 Angle : 0.475 4.495 34188 Z= 0.251 Chirality : 0.044 0.217 3995 Planarity : 0.004 0.036 4361 Dihedral : 6.636 58.764 4072 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.79 % Allowed : 11.87 % Favored : 86.34 % 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: -0.40 (0.15), residues: 3022 helix: 1.78 (0.20), residues: 711 sheet: 0.66 (0.19), residues: 660 loop : -1.68 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 432 HIS 0.003 0.001 HIS B 63 PHE 0.011 0.001 PHE A1117 TYR 0.014 0.001 TYR C1134 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 3.747 Fit side-chains revert: symmetry clash REVERT: C 91 SER cc_start: 0.8584 (p) cc_final: 0.8309 (m) REVERT: C 110 LYS cc_start: 0.6854 (mptt) cc_final: 0.6307 (tptp) REVERT: C 184 ASN cc_start: 0.7065 (m-40) cc_final: 0.6158 (p0) REVERT: C 454 LYS cc_start: 0.8513 (tptp) cc_final: 0.8283 (mppt) REVERT: C 693 MET cc_start: 0.9234 (ptt) cc_final: 0.9004 (ptp) REVERT: A 185 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6938 (mt) REVERT: A 216 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 283 ASP cc_start: 0.8126 (t0) cc_final: 0.7843 (t0) REVERT: A 305 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7490 (mp0) REVERT: A 374 LYS cc_start: 0.8030 (tppp) cc_final: 0.7118 (tptt) REVERT: A 454 LYS cc_start: 0.8468 (mtpm) cc_final: 0.7707 (pmtt) REVERT: A 520 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7452 (p) REVERT: A 525 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7429 (mmtm) REVERT: A 550 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7638 (mm-30) REVERT: A 790 ILE cc_start: 0.8213 (mt) cc_final: 0.7735 (pp) REVERT: A 1006 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7927 (mp10) REVERT: A 1034 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8486 (mmtp) REVERT: A 1114 ASP cc_start: 0.7800 (m-30) cc_final: 0.7571 (m-30) REVERT: A 1118 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8743 (p) REVERT: A 1134 TYR cc_start: 0.8245 (t80) cc_final: 0.7972 (t80) REVERT: B 99 ARG cc_start: 0.6152 (mmm-85) cc_final: 0.5438 (mpt180) REVERT: B 165 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6429 (mm-30) REVERT: B 186 ARG cc_start: 0.6306 (mtt-85) cc_final: 0.5326 (mmp80) REVERT: B 294 GLU cc_start: 0.8013 (tt0) cc_final: 0.7548 (tt0) REVERT: B 310 GLN cc_start: 0.8462 (tt0) cc_final: 0.8192 (tt0) REVERT: B 315 ARG cc_start: 0.7383 (ptp90) cc_final: 0.6701 (ptm160) REVERT: B 362 SER cc_start: 0.9130 (t) cc_final: 0.8877 (m) REVERT: B 374 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7230 (tptt) REVERT: B 410 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 467 GLU cc_start: 0.6632 (mt-10) cc_final: 0.5682 (pp20) REVERT: B 525 LYS cc_start: 0.8155 (mtpm) cc_final: 0.7924 (tttp) REVERT: B 530 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8362 (m) REVERT: B 533 LYS cc_start: 0.8186 (mttm) cc_final: 0.7795 (mtmt) REVERT: B 561 PHE cc_start: 0.7994 (p90) cc_final: 0.7575 (p90) REVERT: B 671 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7204 (mp10) REVERT: B 960 LYS cc_start: 0.8252 (tttt) cc_final: 0.8029 (mtmt) REVERT: B 1046 MET cc_start: 0.8291 (mtp) cc_final: 0.7877 (mtp) outliers start: 48 outliers final: 33 residues processed: 230 average time/residue: 2.5870 time to fit residues: 710.2212 Evaluate side-chains 231 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN C 998 GLN A 953 GLN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25125 Z= 0.230 Angle : 0.496 4.908 34188 Z= 0.262 Chirality : 0.044 0.230 3995 Planarity : 0.004 0.036 4361 Dihedral : 6.635 58.634 4072 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.94 % Allowed : 12.02 % Favored : 86.04 % 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: -0.42 (0.15), residues: 3022 helix: 1.76 (0.20), residues: 711 sheet: 0.65 (0.19), residues: 661 loop : -1.70 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 432 HIS 0.005 0.001 HIS B1060 PHE 0.013 0.001 PHE A1117 TYR 0.015 0.001 TYR B1063 ARG 0.002 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 3.524 Fit side-chains revert: symmetry clash REVERT: C 91 SER cc_start: 0.8586 (p) cc_final: 0.8318 (m) REVERT: C 110 LYS cc_start: 0.6836 (mptt) cc_final: 0.6289 (tptp) REVERT: C 184 ASN cc_start: 0.7036 (m-40) cc_final: 0.6210 (p0) REVERT: C 192 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.5774 (t0) REVERT: C 454 LYS cc_start: 0.8516 (tptp) cc_final: 0.8286 (mppt) REVERT: C 693 MET cc_start: 0.9250 (ptt) cc_final: 0.9025 (ptp) REVERT: A 185 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6942 (mt) REVERT: A 216 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 283 ASP cc_start: 0.8152 (t0) cc_final: 0.7874 (t0) REVERT: A 305 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7443 (mp0) REVERT: A 374 LYS cc_start: 0.8178 (tppp) cc_final: 0.7243 (tptt) REVERT: A 454 LYS cc_start: 0.8477 (mtpm) cc_final: 0.7714 (pmtt) REVERT: A 520 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7478 (p) REVERT: A 525 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7430 (mmtm) REVERT: A 550 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7651 (mm-30) REVERT: A 790 ILE cc_start: 0.8209 (mt) cc_final: 0.7743 (pp) REVERT: A 1006 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7926 (mp10) REVERT: A 1034 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8401 (mmtp) REVERT: A 1114 ASP cc_start: 0.7791 (m-30) cc_final: 0.7560 (m-30) REVERT: A 1118 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8779 (p) REVERT: A 1134 TYR cc_start: 0.8292 (t80) cc_final: 0.8039 (t80) REVERT: B 99 ARG cc_start: 0.6158 (mmm-85) cc_final: 0.5437 (mpt180) REVERT: B 165 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6392 (mm-30) REVERT: B 186 ARG cc_start: 0.6294 (mtt-85) cc_final: 0.5319 (mmp80) REVERT: B 294 GLU cc_start: 0.8029 (tt0) cc_final: 0.7553 (tt0) REVERT: B 310 GLN cc_start: 0.8457 (tt0) cc_final: 0.8209 (tt0) REVERT: B 315 ARG cc_start: 0.7422 (ptp90) cc_final: 0.6748 (ptm160) REVERT: B 362 SER cc_start: 0.9130 (t) cc_final: 0.8880 (m) REVERT: B 374 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7255 (tptt) REVERT: B 410 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: B 467 GLU cc_start: 0.6734 (mt-10) cc_final: 0.5773 (pp20) REVERT: B 525 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7927 (tttp) REVERT: B 530 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8394 (m) REVERT: B 533 LYS cc_start: 0.8203 (mttm) cc_final: 0.7815 (mtmt) REVERT: B 561 PHE cc_start: 0.8006 (p90) cc_final: 0.7580 (p90) REVERT: B 671 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7082 (mp10) REVERT: B 960 LYS cc_start: 0.8277 (tttt) cc_final: 0.8055 (mtmt) REVERT: B 998 GLN cc_start: 0.8191 (tp40) cc_final: 0.7866 (mm-40) REVERT: B 1046 MET cc_start: 0.8337 (mtp) cc_final: 0.7929 (mtp) outliers start: 52 outliers final: 37 residues processed: 230 average time/residue: 2.5568 time to fit residues: 692.4756 Evaluate side-chains 232 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 0.0050 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN C 998 GLN A 953 GLN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25125 Z= 0.179 Angle : 0.474 5.054 34188 Z= 0.249 Chirality : 0.043 0.219 3995 Planarity : 0.004 0.035 4361 Dihedral : 6.438 58.561 4072 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.79 % Allowed : 12.39 % Favored : 85.82 % 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: -0.35 (0.15), residues: 3022 helix: 1.85 (0.20), residues: 711 sheet: 0.69 (0.19), residues: 660 loop : -1.67 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 432 HIS 0.003 0.001 HIS B1060 PHE 0.011 0.001 PHE A1117 TYR 0.015 0.001 TYR C1134 ARG 0.002 0.000 ARG A 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6044 Ramachandran restraints generated. 3022 Oldfield, 0 Emsley, 3022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 SER cc_start: 0.8579 (p) cc_final: 0.8321 (m) REVERT: C 110 LYS cc_start: 0.6850 (mptt) cc_final: 0.6285 (tptp) REVERT: C 184 ASN cc_start: 0.7026 (m-40) cc_final: 0.6215 (p0) REVERT: C 192 ASN cc_start: 0.6387 (OUTLIER) cc_final: 0.5748 (t0) REVERT: C 454 LYS cc_start: 0.8513 (tptp) cc_final: 0.8282 (mppt) REVERT: C 693 MET cc_start: 0.9233 (ptt) cc_final: 0.9005 (ptp) REVERT: A 185 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6935 (mt) REVERT: A 216 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6655 (t80) REVERT: A 283 ASP cc_start: 0.8132 (t0) cc_final: 0.7822 (t0) REVERT: A 305 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7461 (mp0) REVERT: A 374 LYS cc_start: 0.8141 (tppp) cc_final: 0.7210 (tptt) REVERT: A 454 LYS cc_start: 0.8477 (mtpm) cc_final: 0.7714 (pmtt) REVERT: A 520 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7433 (p) REVERT: A 525 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7427 (mmtm) REVERT: A 550 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7635 (mm-30) REVERT: A 790 ILE cc_start: 0.8207 (mt) cc_final: 0.7733 (pp) REVERT: A 1006 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7900 (mp10) REVERT: A 1034 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8399 (mmtp) REVERT: A 1114 ASP cc_start: 0.7770 (m-30) cc_final: 0.7538 (m-30) REVERT: A 1118 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 1134 TYR cc_start: 0.8291 (t80) cc_final: 0.8035 (t80) REVERT: B 99 ARG cc_start: 0.6137 (mmm-85) cc_final: 0.5413 (mpt180) REVERT: B 165 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6405 (mm-30) REVERT: B 186 ARG cc_start: 0.6295 (mtt-85) cc_final: 0.5322 (mmp80) REVERT: B 294 GLU cc_start: 0.8018 (tt0) cc_final: 0.7547 (tt0) REVERT: B 310 GLN cc_start: 0.8455 (tt0) cc_final: 0.8165 (tt0) REVERT: B 315 ARG cc_start: 0.7394 (ptp90) cc_final: 0.6700 (ptm160) REVERT: B 362 SER cc_start: 0.9122 (t) cc_final: 0.8885 (m) REVERT: B 374 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7313 (tptt) REVERT: B 410 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: B 467 GLU cc_start: 0.6696 (mt-10) cc_final: 0.5737 (pp20) REVERT: B 486 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7198 (p) REVERT: B 525 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7926 (tttp) REVERT: B 530 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8357 (m) REVERT: B 533 LYS cc_start: 0.8175 (mttm) cc_final: 0.7795 (mtmt) REVERT: B 561 PHE cc_start: 0.7922 (p90) cc_final: 0.7554 (p90) REVERT: B 671 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7068 (mp10) REVERT: B 960 LYS cc_start: 0.8241 (tttt) cc_final: 0.8021 (mtmt) REVERT: B 1046 MET cc_start: 0.8312 (mtp) cc_final: 0.7912 (mtp) outliers start: 48 outliers final: 35 residues processed: 227 average time/residue: 2.6712 time to fit residues: 721.9539 Evaluate side-chains 231 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 830 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 213 optimal weight: 0.0980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN C 998 GLN A 953 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110892 restraints weight = 91827.287| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.02 r_work: 0.3195 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25125 Z= 0.141 Angle : 0.456 6.512 34188 Z= 0.239 Chirality : 0.043 0.203 3995 Planarity : 0.003 0.034 4361 Dihedral : 6.125 58.931 4072 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.38 % Allowed : 12.77 % Favored : 85.86 % 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: -0.16 (0.15), residues: 3022 helix: 2.12 (0.21), residues: 702 sheet: 0.77 (0.19), residues: 662 loop : -1.57 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 432 HIS 0.003 0.000 HIS B 63 PHE 0.009 0.001 PHE A1117 TYR 0.016 0.001 TYR C1134 ARG 0.003 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13909.17 seconds wall clock time: 242 minutes 3.50 seconds (14523.50 seconds total)