Starting phenix.real_space_refine on Tue Mar 19 08:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyo_23597/03_2024/7lyo_23597.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 15098 2.51 5 N 3886 2.21 5 O 4561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7707 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7705 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 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 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 11.68, per 1000 atoms: 0.49 Number of scatterers: 23649 At special positions: 0 Unit cell: (125.073, 134.694, 194.558, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4561 8.00 N 3886 7.00 C 15098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 801 " " NAG A1313 " - " ASN A1074 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1098 " " NAG C1313 " - " ASN C1134 " Time building additional restraints: 9.12 Conformation dependent library (CDL) restraints added in 4.0 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5574 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 46 sheets defined 27.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.522A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.711A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.182A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.871A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.633A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.901A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.547A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.708A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.176A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.037A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.102A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.411A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.898A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.588A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.606A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.667A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.708A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.347A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.848A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.593A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.814A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.844A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.816A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.568A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.920A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.519A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.542A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.321A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.737A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.793A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.679A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.377A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.172A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.557A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.557A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.778A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.352A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.352A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.362A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.486A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.629A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.939A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.334A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.965A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.638A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.638A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.243A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.650A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.608A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.771A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.142A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.512A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.790A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.715A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.708A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.008A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.874A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2829 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: 10.13 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5932 1.33 - 1.45: 4747 1.45 - 1.58: 13355 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 24162 Sorted by residual: bond pdb=" C5 NAG C1313 " pdb=" O5 NAG C1313 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.23: 300 104.23 - 111.96: 10000 111.96 - 119.69: 10201 119.69 - 127.43: 12228 127.43 - 135.16: 153 Bond angle restraints: 32882 Sorted by residual: angle pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " ideal model delta sigma weight residual 112.60 119.58 -6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.47 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CB ASN B 801 " pdb=" CG ASN B 801 " pdb=" ND2 ASN B 801 " ideal model delta sigma weight residual 116.40 124.73 -8.33 1.50e+00 4.44e-01 3.08e+01 ... (remaining 32877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13900 17.90 - 35.80: 753 35.80 - 53.70: 153 53.70 - 71.60: 41 71.60 - 89.50: 19 Dihedral angle restraints: 14866 sinusoidal: 6205 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -177.98 -89.02 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA THR B 581 " pdb=" C THR B 581 " pdb=" N LEU B 582 " pdb=" CA LEU B 582 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 14863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2773 0.101 - 0.202: 1012 0.202 - 0.304: 97 0.304 - 0.405: 12 0.405 - 0.506: 1 Chirality restraints: 3895 Sorted by residual: chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA TYR B 200 " pdb=" N TYR B 200 " pdb=" C TYR B 200 " pdb=" CB TYR B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3892 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.283 2.00e-02 2.50e+03 1.50e-01 5.63e+02 pdb=" CG TRP C 886 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.137 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.216 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.169 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.132 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C 61 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.137 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN A 331 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.172 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11463 2.99 - 3.47: 22482 3.47 - 3.94: 38969 3.94 - 4.42: 43289 4.42 - 4.90: 73983 Nonbonded interactions: 190186 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.511 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.517 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.528 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.533 2.440 ... (remaining 190181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name \ CA or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 567 or (resid 568 and (name N or name CA or na \ me C or name O or name CB )) or resid 569 through 582 or (resid 583 and (name N \ or name CA or name C or name O or name CB )) or resid 584 through 585 or (resid \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name \ CA or name C or name O or name CB )) or resid 746 through 747 or (resid 748 and \ (name N or name CA or name C or name O or name CB )) or resid 749 through 810 o \ r (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 13 or (resid 814 and (name N or name CA or name C or name O or name CB )) or res \ id 815 through 827 or resid 855 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 1091 or (res \ id 1092 and (name N or name CA or name C or name O or name CB )) or resid 1093 t \ hrough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147 or resid 1301 through 1312)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or na \ me O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (n \ ame N or name CA or name C or name O or name CB )) or resid 310 through 527 or ( \ resid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 \ through 567 or (resid 568 and (name N or name CA or name C or name O or name CB \ )) or resid 569 through 582 or (resid 583 and (name N or name CA or name C or na \ me O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and (n \ ame N or name CA or name C or name O or name CB )) or resid 620 through 813 or ( \ resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name C \ B )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1 \ 312)) } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.130 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 62.220 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.130 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.013 0.076 24162 Z= 0.863 Angle : 1.750 10.041 32882 Z= 1.176 Chirality : 0.095 0.506 3895 Planarity : 0.013 0.165 4184 Dihedral : 12.468 89.504 9175 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.43 % Favored : 94.30 % Rotamer: Outliers : 0.43 % Allowed : 2.31 % Favored : 97.25 % Cbeta Deviations : 0.18 % 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: -0.89 (0.14), residues: 2928 helix: -1.05 (0.17), residues: 703 sheet: 0.58 (0.21), residues: 523 loop : -0.72 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.283 0.029 TRP C 886 HIS 0.009 0.003 HIS A1048 PHE 0.086 0.012 PHE C 718 TYR 0.126 0.019 TYR B 421 ARG 0.011 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 392 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 SER cc_start: 0.7600 (t) cc_final: 0.7069 (t) REVERT: A 394 ASN cc_start: 0.7480 (m-40) cc_final: 0.7253 (m-40) REVERT: A 902 MET cc_start: 0.8632 (mmm) cc_final: 0.8383 (mmm) REVERT: A 950 ASP cc_start: 0.7531 (t70) cc_final: 0.7227 (t0) REVERT: B 54 LEU cc_start: 0.8457 (mt) cc_final: 0.8249 (mp) REVERT: B 347 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.3408 (m-80) REVERT: B 392 PHE cc_start: 0.7502 (m-80) cc_final: 0.7102 (m-10) REVERT: B 572 THR cc_start: 0.8849 (m) cc_final: 0.8333 (m) REVERT: C 428 ASP cc_start: 0.7342 (p0) cc_final: 0.6675 (t70) REVERT: C 469 SER cc_start: 0.7906 (t) cc_final: 0.7602 (m) REVERT: C 902 MET cc_start: 0.8860 (mmm) cc_final: 0.8515 (tpt) REVERT: C 904 TYR cc_start: 0.7874 (m-10) cc_final: 0.7459 (m-10) outliers start: 11 outliers final: 4 residues processed: 401 average time/residue: 0.3722 time to fit residues: 228.5121 Evaluate side-chains 194 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 347 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 61 ASN B 87 ASN B 762 GLN B 914 ASN B1088 HIS C 207 HIS C 556 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1002 GLN C1113 GLN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24162 Z= 0.261 Angle : 0.633 8.032 32882 Z= 0.334 Chirality : 0.047 0.231 3895 Planarity : 0.004 0.035 4184 Dihedral : 7.535 59.132 4032 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.39 % Favored : 97.40 % Rotamer: Outliers : 1.57 % Allowed : 6.94 % Favored : 91.49 % 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: -0.00 (0.15), residues: 2928 helix: 0.98 (0.20), residues: 689 sheet: 0.36 (0.19), residues: 687 loop : -0.58 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.005 0.001 HIS C1083 PHE 0.023 0.002 PHE A 140 TYR 0.024 0.002 TYR B 369 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7690 (m-40) cc_final: 0.7091 (m110) REVERT: A 428 ASP cc_start: 0.8315 (p0) cc_final: 0.8034 (p0) REVERT: A 470 THR cc_start: 0.8773 (p) cc_final: 0.8409 (t) REVERT: A 776 LYS cc_start: 0.8562 (tttt) cc_final: 0.8227 (tttm) REVERT: A 957 GLN cc_start: 0.7988 (tp40) cc_final: 0.7676 (tp40) REVERT: A 1051 SER cc_start: 0.9008 (p) cc_final: 0.8784 (m) REVERT: B 347 PHE cc_start: 0.4633 (OUTLIER) cc_final: 0.3368 (m-80) REVERT: B 392 PHE cc_start: 0.7474 (m-80) cc_final: 0.7074 (m-10) REVERT: B 515 PHE cc_start: 0.7646 (m-10) cc_final: 0.7377 (m-10) REVERT: B 950 ASP cc_start: 0.7980 (t0) cc_final: 0.7687 (t0) REVERT: C 465 GLU cc_start: 0.7363 (tt0) cc_final: 0.6876 (mt-10) REVERT: C 469 SER cc_start: 0.8110 (t) cc_final: 0.7840 (m) REVERT: C 900 MET cc_start: 0.8359 (mtp) cc_final: 0.7866 (mtp) REVERT: C 904 TYR cc_start: 0.7726 (m-10) cc_final: 0.7107 (m-10) outliers start: 40 outliers final: 22 residues processed: 237 average time/residue: 0.3294 time to fit residues: 125.6169 Evaluate side-chains 174 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN B 394 ASN C 218 GLN C 317 ASN C 901 GLN C1088 HIS C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 24162 Z= 0.343 Angle : 0.608 11.842 32882 Z= 0.318 Chirality : 0.047 0.239 3895 Planarity : 0.004 0.036 4184 Dihedral : 6.934 59.585 4025 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.69 % Rotamer: Outliers : 2.04 % Allowed : 8.39 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2928 helix: 1.00 (0.20), residues: 696 sheet: 0.34 (0.19), residues: 712 loop : -0.56 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.011 0.001 HIS C 207 PHE 0.025 0.002 PHE B 201 TYR 0.021 0.002 TYR C 369 ARG 0.010 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 167 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9326 (t) cc_final: 0.9016 (p) REVERT: A 414 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 428 ASP cc_start: 0.8395 (p0) cc_final: 0.8076 (p0) REVERT: A 470 THR cc_start: 0.8821 (p) cc_final: 0.8526 (t) REVERT: A 776 LYS cc_start: 0.8472 (tttt) cc_final: 0.8122 (tttm) REVERT: B 135 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5746 (t80) REVERT: B 281 GLU cc_start: 0.7366 (pm20) cc_final: 0.7159 (pm20) REVERT: B 347 PHE cc_start: 0.4648 (OUTLIER) cc_final: 0.3396 (m-80) REVERT: B 392 PHE cc_start: 0.7374 (m-80) cc_final: 0.6996 (m-10) REVERT: C 465 GLU cc_start: 0.7273 (tt0) cc_final: 0.6892 (mt-10) REVERT: C 469 SER cc_start: 0.8156 (t) cc_final: 0.7853 (m) REVERT: C 902 MET cc_start: 0.8618 (mmt) cc_final: 0.8402 (tpt) outliers start: 52 outliers final: 33 residues processed: 208 average time/residue: 0.3183 time to fit residues: 109.4519 Evaluate side-chains 178 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.0050 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN C 188 ASN C 218 GLN C1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24162 Z= 0.194 Angle : 0.534 9.313 32882 Z= 0.276 Chirality : 0.045 0.515 3895 Planarity : 0.003 0.041 4184 Dihedral : 6.704 58.608 4025 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 2.00 % Allowed : 9.57 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2928 helix: 1.40 (0.20), residues: 689 sheet: 0.28 (0.18), residues: 706 loop : -0.40 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS B1083 PHE 0.024 0.001 PHE B 168 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9354 (t) cc_final: 0.9033 (p) REVERT: A 414 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7991 (mm-40) REVERT: A 428 ASP cc_start: 0.8365 (p0) cc_final: 0.8053 (p0) REVERT: A 470 THR cc_start: 0.8826 (p) cc_final: 0.8549 (t) REVERT: A 776 LYS cc_start: 0.8519 (tttt) cc_final: 0.8176 (tttm) REVERT: A 1051 SER cc_start: 0.8957 (p) cc_final: 0.8729 (m) REVERT: A 1096 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8954 (p) REVERT: B 135 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5862 (t80) REVERT: B 269 TYR cc_start: 0.6978 (m-10) cc_final: 0.6698 (m-80) REVERT: B 347 PHE cc_start: 0.4665 (OUTLIER) cc_final: 0.3517 (m-80) REVERT: B 392 PHE cc_start: 0.7429 (m-80) cc_final: 0.7100 (m-10) REVERT: C 129 LYS cc_start: 0.7554 (tttt) cc_final: 0.7289 (ttmt) REVERT: C 309 GLU cc_start: 0.7539 (mp0) cc_final: 0.7270 (mp0) REVERT: C 428 ASP cc_start: 0.7879 (p0) cc_final: 0.6771 (t70) REVERT: C 465 GLU cc_start: 0.7255 (tt0) cc_final: 0.6848 (mt-10) REVERT: C 855 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5432 (m-80) outliers start: 51 outliers final: 27 residues processed: 212 average time/residue: 0.3200 time to fit residues: 111.4906 Evaluate side-chains 178 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN C 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 24162 Z= 0.509 Angle : 0.651 15.163 32882 Z= 0.335 Chirality : 0.049 0.506 3895 Planarity : 0.004 0.046 4184 Dihedral : 7.000 59.014 4025 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 10.51 % Favored : 87.14 % 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: -0.08 (0.15), residues: 2928 helix: 1.00 (0.20), residues: 687 sheet: 0.17 (0.18), residues: 709 loop : -0.60 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.007 0.001 HIS A1064 PHE 0.028 0.002 PHE B 168 TYR 0.023 0.002 TYR C1067 ARG 0.007 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 151 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9384 (t) cc_final: 0.9101 (p) REVERT: A 319 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7330 (mtp-110) REVERT: A 414 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7984 (mm-40) REVERT: A 428 ASP cc_start: 0.8435 (p0) cc_final: 0.8102 (p0) REVERT: A 470 THR cc_start: 0.8820 (p) cc_final: 0.8515 (t) REVERT: A 776 LYS cc_start: 0.8520 (tttt) cc_final: 0.8289 (tttm) REVERT: A 869 MET cc_start: 0.8852 (mtm) cc_final: 0.8524 (mtt) REVERT: B 135 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.6031 (t80) REVERT: B 235 ILE cc_start: 0.3181 (OUTLIER) cc_final: 0.2947 (mp) REVERT: B 269 TYR cc_start: 0.7053 (m-10) cc_final: 0.6791 (m-80) REVERT: B 347 PHE cc_start: 0.4774 (OUTLIER) cc_final: 0.3515 (m-80) REVERT: B 392 PHE cc_start: 0.7425 (m-80) cc_final: 0.7084 (m-10) REVERT: C 129 LYS cc_start: 0.7682 (tttt) cc_final: 0.7445 (tttm) REVERT: C 452 LEU cc_start: 0.8639 (mp) cc_final: 0.8372 (mt) REVERT: C 465 GLU cc_start: 0.7225 (tt0) cc_final: 0.6793 (mt-10) REVERT: C 469 SER cc_start: 0.8179 (t) cc_final: 0.7878 (m) REVERT: C 855 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5693 (m-80) outliers start: 60 outliers final: 46 residues processed: 201 average time/residue: 0.3002 time to fit residues: 101.6177 Evaluate side-chains 187 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 137 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 0.0670 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1083 HIS C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24162 Z= 0.161 Angle : 0.506 12.391 32882 Z= 0.261 Chirality : 0.044 0.371 3895 Planarity : 0.003 0.037 4184 Dihedral : 6.509 58.101 4025 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 1.80 % Allowed : 11.57 % Favored : 86.63 % 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: 2928 helix: 1.61 (0.21), residues: 678 sheet: 0.21 (0.19), residues: 675 loop : -0.45 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.004 0.001 HIS B1083 PHE 0.026 0.001 PHE B 168 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9362 (t) cc_final: 0.9106 (p) REVERT: A 414 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8019 (mm-40) REVERT: A 428 ASP cc_start: 0.8351 (p0) cc_final: 0.8052 (p0) REVERT: A 470 THR cc_start: 0.8881 (p) cc_final: 0.8614 (t) REVERT: A 776 LYS cc_start: 0.8473 (tttt) cc_final: 0.8260 (tttm) REVERT: A 869 MET cc_start: 0.8736 (mtm) cc_final: 0.8515 (mtt) REVERT: B 269 TYR cc_start: 0.6839 (m-10) cc_final: 0.6577 (m-80) REVERT: B 347 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.3566 (m-80) REVERT: C 465 GLU cc_start: 0.7146 (tt0) cc_final: 0.6774 (mt-10) REVERT: C 469 SER cc_start: 0.8180 (t) cc_final: 0.7909 (m) REVERT: C 855 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5552 (m-80) outliers start: 46 outliers final: 31 residues processed: 205 average time/residue: 0.3024 time to fit residues: 104.7450 Evaluate side-chains 170 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 160 optimal weight: 0.0970 chunk 286 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 0.0570 chunk 132 optimal weight: 7.9990 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24162 Z= 0.199 Angle : 0.515 11.999 32882 Z= 0.265 Chirality : 0.044 0.337 3895 Planarity : 0.003 0.039 4184 Dihedral : 6.377 57.234 4025 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.21 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 12.00 % Favored : 86.12 % 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: 0.34 (0.15), residues: 2928 helix: 1.70 (0.21), residues: 684 sheet: 0.30 (0.19), residues: 680 loop : -0.44 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.002 0.001 HIS A1064 PHE 0.026 0.001 PHE B 168 TYR 0.018 0.001 TYR B1067 ARG 0.011 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9383 (t) cc_final: 0.9136 (p) REVERT: A 414 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8018 (mm-40) REVERT: A 428 ASP cc_start: 0.8333 (p0) cc_final: 0.8076 (p0) REVERT: A 470 THR cc_start: 0.8825 (p) cc_final: 0.8553 (t) REVERT: B 135 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5715 (t80) REVERT: B 269 TYR cc_start: 0.6781 (m-10) cc_final: 0.6536 (m-80) REVERT: B 347 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.3389 (m-80) REVERT: C 452 LEU cc_start: 0.8630 (mp) cc_final: 0.8404 (mt) REVERT: C 465 GLU cc_start: 0.7124 (tt0) cc_final: 0.6756 (mt-10) REVERT: C 469 SER cc_start: 0.8103 (t) cc_final: 0.7832 (m) REVERT: C 855 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5543 (m-80) outliers start: 48 outliers final: 40 residues processed: 195 average time/residue: 0.2857 time to fit residues: 95.6511 Evaluate side-chains 186 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24162 Z= 0.265 Angle : 0.536 11.549 32882 Z= 0.275 Chirality : 0.045 0.310 3895 Planarity : 0.003 0.040 4184 Dihedral : 6.376 59.342 4025 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 2.08 % Allowed : 12.51 % Favored : 85.41 % 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: 0.31 (0.15), residues: 2928 helix: 1.64 (0.21), residues: 679 sheet: 0.30 (0.19), residues: 707 loop : -0.46 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.004 0.001 HIS C1048 PHE 0.027 0.002 PHE B 168 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9392 (t) cc_final: 0.9161 (p) REVERT: A 318 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 414 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8050 (mm-40) REVERT: A 428 ASP cc_start: 0.8368 (p0) cc_final: 0.8100 (p0) REVERT: A 470 THR cc_start: 0.8834 (p) cc_final: 0.8556 (t) REVERT: B 118 LEU cc_start: 0.8314 (tp) cc_final: 0.8098 (tp) REVERT: B 269 TYR cc_start: 0.6799 (m-10) cc_final: 0.6512 (m-80) REVERT: B 347 PHE cc_start: 0.4725 (OUTLIER) cc_final: 0.3466 (m-80) REVERT: C 452 LEU cc_start: 0.8730 (mp) cc_final: 0.8505 (mt) REVERT: C 465 GLU cc_start: 0.7118 (tt0) cc_final: 0.6746 (mt-10) REVERT: C 469 SER cc_start: 0.8091 (t) cc_final: 0.7842 (m) REVERT: C 855 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 904 TYR cc_start: 0.7741 (m-10) cc_final: 0.7344 (m-10) outliers start: 53 outliers final: 45 residues processed: 190 average time/residue: 0.2799 time to fit residues: 92.1963 Evaluate side-chains 185 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 0.0970 chunk 160 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24162 Z= 0.180 Angle : 0.502 11.322 32882 Z= 0.257 Chirality : 0.044 0.320 3895 Planarity : 0.003 0.036 4184 Dihedral : 6.169 57.030 4025 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.96 % Allowed : 12.78 % Favored : 85.25 % 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: 2928 helix: 1.78 (0.21), residues: 687 sheet: 0.34 (0.19), residues: 693 loop : -0.40 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.002 0.001 HIS B1083 PHE 0.024 0.001 PHE B 168 TYR 0.019 0.001 TYR C 489 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7471 (p90) REVERT: A 414 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 428 ASP cc_start: 0.8319 (p0) cc_final: 0.8083 (p0) REVERT: A 470 THR cc_start: 0.8826 (p) cc_final: 0.8549 (t) REVERT: B 118 LEU cc_start: 0.8212 (tp) cc_final: 0.7984 (tp) REVERT: B 347 PHE cc_start: 0.4605 (OUTLIER) cc_final: 0.3437 (m-80) REVERT: B 392 PHE cc_start: 0.6707 (m-10) cc_final: 0.6211 (m-10) REVERT: C 452 LEU cc_start: 0.8715 (mp) cc_final: 0.8506 (mt) REVERT: C 465 GLU cc_start: 0.7069 (tt0) cc_final: 0.6698 (mt-10) REVERT: C 469 SER cc_start: 0.8042 (t) cc_final: 0.7814 (m) REVERT: C 855 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.5580 (m-80) outliers start: 50 outliers final: 42 residues processed: 197 average time/residue: 0.2780 time to fit residues: 94.5620 Evaluate side-chains 187 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 133 optimal weight: 30.0000 chunk 196 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 272 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24162 Z= 0.174 Angle : 0.505 11.241 32882 Z= 0.258 Chirality : 0.044 0.311 3895 Planarity : 0.003 0.035 4184 Dihedral : 6.087 56.582 4025 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 1.92 % Allowed : 13.14 % Favored : 84.94 % 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: 0.46 (0.15), residues: 2928 helix: 1.80 (0.20), residues: 690 sheet: 0.37 (0.19), residues: 697 loop : -0.38 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.002 0.001 HIS B1083 PHE 0.026 0.001 PHE B 515 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7394 (p90) REVERT: A 326 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7432 (mm) REVERT: A 414 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7993 (mm-40) REVERT: A 428 ASP cc_start: 0.8308 (p0) cc_final: 0.8088 (p0) REVERT: A 470 THR cc_start: 0.8850 (p) cc_final: 0.8586 (t) REVERT: B 118 LEU cc_start: 0.8183 (tp) cc_final: 0.7965 (tp) REVERT: B 229 LEU cc_start: 0.8239 (tt) cc_final: 0.8037 (tt) REVERT: B 347 PHE cc_start: 0.4598 (OUTLIER) cc_final: 0.3455 (m-80) REVERT: C 465 GLU cc_start: 0.7028 (tt0) cc_final: 0.6676 (mt-10) REVERT: C 469 SER cc_start: 0.8000 (t) cc_final: 0.7774 (m) REVERT: C 855 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5542 (m-80) outliers start: 49 outliers final: 40 residues processed: 194 average time/residue: 0.2855 time to fit residues: 95.4844 Evaluate side-chains 185 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 235 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109982 restraints weight = 33595.873| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.66 r_work: 0.3048 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24162 Z= 0.332 Angle : 0.565 11.149 32882 Z= 0.288 Chirality : 0.046 0.305 3895 Planarity : 0.003 0.032 4184 Dihedral : 6.305 59.933 4025 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 2.08 % Allowed : 13.02 % Favored : 84.90 % 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: 0.31 (0.15), residues: 2928 helix: 1.59 (0.20), residues: 685 sheet: 0.35 (0.19), residues: 699 loop : -0.45 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.005 0.001 HIS A1064 PHE 0.039 0.002 PHE B 392 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4255.16 seconds wall clock time: 78 minutes 26.01 seconds (4706.01 seconds total)