Starting phenix.real_space_refine on Thu Apr 11 23:45:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r15_14231/04_2024/7r15_14231.pdb" } resolution = 4.1 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= 0.004 sd= 0.062 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 15377 2.51 5 N 3950 2.21 5 O 4669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24100 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7702 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 51, 'TRANS': 931} Chain breaks: 9 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7988 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 50, 'TRANS': 969} Chain breaks: 8 Chain: "C" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7808 Classifications: {'peptide': 997} Link IDs: {'PTRANS': 51, 'TRANS': 945} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 11.99, per 1000 atoms: 0.50 Number of scatterers: 24100 At special positions: 0 Unit cell: (139.136, 136.962, 198.921, 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 4669 8.00 N 3950 7.00 C 15377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 343 " " NAG A1311 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 343 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C1098 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 331 " Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 4.0 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 50 sheets defined 23.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.368A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.656A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 removed outlier: 3.718A pdb=" N GLY A 799 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.632A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.536A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.759A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.565A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.868A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 4.093A pdb=" N SER B 375 " --> pdb=" O ALA B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.557A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.717A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 780 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.755A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.869A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 948 through 967 removed outlier: 3.884A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.705A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.768A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 5.478A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.499A 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 737 through 743 removed outlier: 3.825A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.549A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.930A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.768A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.714A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.947A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.535A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.037A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.195A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.519A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.689A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.100A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 removed outlier: 3.776A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 317 removed outlier: 5.789A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.684A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.557A pdb=" N LYS A 424 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.159A pdb=" N ASN A 450 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLN A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.777A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.975A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.227A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.681A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 5.923A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.588A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.356A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.995A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.661A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.023A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.573A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.668A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 660 through 661 removed outlier: 6.390A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.512A pdb=" N PHE B1075 " --> pdb=" O ILE B 712 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.811A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.561A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.509A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.564A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.776A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.730A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.982A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 598 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.834A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.079A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.550A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.550A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.757A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.757A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 6.036A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2223 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: 10.83 Time building geometry restraints manager: 10.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7653 1.34 - 1.46: 5374 1.46 - 1.58: 11482 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24638 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 24633 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.90: 534 105.90 - 112.92: 13404 112.92 - 119.94: 8007 119.94 - 126.96: 11351 126.96 - 133.98: 219 Bond angle restraints: 33515 Sorted by residual: angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.53 110.22 3.31 9.80e-01 1.04e+00 1.14e+01 angle pdb=" OG1 THR C 618 " pdb=" CB THR C 618 " pdb=" CG2 THR C 618 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" C ASN C 196 " pdb=" CA ASN C 196 " pdb=" CB ASN C 196 " ideal model delta sigma weight residual 110.14 114.74 -4.60 1.54e+00 4.22e-01 8.92e+00 ... (remaining 33510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 14329 23.30 - 46.60: 726 46.60 - 69.90: 136 69.90 - 93.20: 37 93.20 - 116.50: 3 Dihedral angle restraints: 15231 sinusoidal: 6504 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -4.36 -81.64 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 158.72 -65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -29.85 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 15228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3519 0.079 - 0.159: 396 0.159 - 0.238: 6 0.238 - 0.318: 0 0.318 - 0.397: 5 Chirality restraints: 3926 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3923 not shown) Planarity restraints: 4324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 196 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASN C 196 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN C 196 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 197 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO C 987 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 295 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.028 5.00e-02 4.00e+02 ... (remaining 4321 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 471 2.66 - 3.22: 23523 3.22 - 3.78: 37316 3.78 - 4.34: 48127 4.34 - 4.90: 77070 Nonbonded interactions: 186507 Sorted by model distance: nonbonded pdb=" O ASP A 294 " pdb=" OG SER A 297 " model vdw 2.099 2.440 nonbonded pdb=" O GLN A 965 " pdb=" OG SER A 968 " model vdw 2.142 2.440 nonbonded pdb=" OG SER A 816 " pdb=" OE1 GLU A 819 " model vdw 2.144 2.440 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.170 2.440 nonbonded pdb=" OG1 THR B 376 " pdb=" NZ LYS B 378 " model vdw 2.171 2.520 ... (remaining 186502 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 26 through 94 or resid 99 through 175 or resid 188 through \ 619 or resid 642 through 826 or resid 854 through 1146 or resid 1301 through 13 \ 11)) selection = (chain 'B' and (resid 26 through 67 or resid 79 through 94 or resid 99 through 1 \ 06 or resid 115 through 135 or resid 169 through 175 or resid 188 through 241 or \ resid 264 through 619 or resid 642 through 826 or resid 854 through 939 or resi \ d 944 through 1146 or resid 1301 through 1311)) selection = (chain 'C' and (resid 26 through 106 or resid 115 through 135 or resid 169 throu \ gh 241 or resid 264 through 619 or resid 642 through 826 or resid 854 through 11 \ 46 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 14.310 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 63.020 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.160 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24638 Z= 0.273 Angle : 0.567 7.692 33515 Z= 0.290 Chirality : 0.045 0.397 3926 Planarity : 0.004 0.054 4284 Dihedral : 14.184 116.501 9495 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.90 (0.15), residues: 2942 helix: 1.59 (0.22), residues: 614 sheet: -0.37 (0.22), residues: 562 loop : -1.55 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.006 0.001 HIS C 49 PHE 0.020 0.001 PHE C 329 TYR 0.012 0.001 TYR C 707 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8239 (t0) cc_final: 0.7957 (t0) REVERT: A 392 PHE cc_start: 0.8303 (m-10) cc_final: 0.8098 (m-10) REVERT: A 740 MET cc_start: 0.8054 (tmm) cc_final: 0.7718 (tmm) REVERT: A 901 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 216 LEU cc_start: 0.7984 (mm) cc_final: 0.7695 (tt) REVERT: B 429 PHE cc_start: 0.9142 (t80) cc_final: 0.8427 (t80) REVERT: B 1050 MET cc_start: 0.8625 (ptt) cc_final: 0.8374 (ptt) REVERT: B 1142 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8935 (tm-30) REVERT: C 118 LEU cc_start: 0.8480 (mp) cc_final: 0.8273 (mp) REVERT: C 275 PHE cc_start: 0.8133 (m-80) cc_final: 0.7205 (m-80) REVERT: C 342 PHE cc_start: 0.9348 (m-80) cc_final: 0.9016 (m-80) REVERT: C 369 TYR cc_start: 0.9166 (t80) cc_final: 0.8933 (t80) REVERT: C 456 PHE cc_start: 0.8927 (m-10) cc_final: 0.8508 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3362 time to fit residues: 100.1594 Evaluate side-chains 108 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 152 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 271 optimal weight: 0.2980 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 658 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24638 Z= 0.225 Angle : 0.541 10.463 33515 Z= 0.281 Chirality : 0.045 0.442 3926 Planarity : 0.004 0.053 4284 Dihedral : 7.449 86.304 4109 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.11 % Allowed : 5.11 % Favored : 94.78 % 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: -0.90 (0.15), residues: 2942 helix: 1.67 (0.22), residues: 634 sheet: -0.48 (0.22), residues: 565 loop : -1.59 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.005 0.001 HIS A1088 PHE 0.020 0.001 PHE C 275 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8269 (t0) cc_final: 0.7977 (t0) REVERT: A 740 MET cc_start: 0.8167 (tmm) cc_final: 0.7941 (tmm) REVERT: A 901 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 117 LEU cc_start: 0.9133 (tp) cc_final: 0.8926 (tp) REVERT: B 201 PHE cc_start: 0.8805 (t80) cc_final: 0.8433 (t80) REVERT: B 216 LEU cc_start: 0.8077 (mm) cc_final: 0.7810 (tt) REVERT: B 429 PHE cc_start: 0.9322 (t80) cc_final: 0.8620 (t80) REVERT: B 740 MET cc_start: 0.8451 (ttm) cc_final: 0.7598 (ttm) REVERT: B 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8649 (tpp) REVERT: B 1050 MET cc_start: 0.8749 (ptt) cc_final: 0.8424 (ptt) REVERT: C 275 PHE cc_start: 0.8383 (m-80) cc_final: 0.7581 (m-80) REVERT: C 342 PHE cc_start: 0.9343 (m-80) cc_final: 0.8993 (m-80) REVERT: C 369 TYR cc_start: 0.9068 (t80) cc_final: 0.8860 (t80) REVERT: C 456 PHE cc_start: 0.8888 (m-10) cc_final: 0.8466 (m-10) REVERT: C 965 GLN cc_start: 0.9023 (tp40) cc_final: 0.8617 (mm110) REVERT: C 1029 MET cc_start: 0.9159 (tpp) cc_final: 0.8787 (tpp) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.3075 time to fit residues: 93.2923 Evaluate side-chains 113 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 218 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24638 Z= 0.198 Angle : 0.520 10.928 33515 Z= 0.269 Chirality : 0.044 0.426 3926 Planarity : 0.004 0.052 4284 Dihedral : 6.908 78.681 4109 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.03 % 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: -0.87 (0.15), residues: 2942 helix: 1.65 (0.22), residues: 635 sheet: -0.49 (0.21), residues: 579 loop : -1.55 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS A1088 PHE 0.018 0.001 PHE C 329 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8282 (t0) cc_final: 0.7959 (t0) REVERT: A 429 PHE cc_start: 0.7276 (t80) cc_final: 0.7070 (t80) REVERT: A 740 MET cc_start: 0.8200 (tmm) cc_final: 0.7958 (tmm) REVERT: B 117 LEU cc_start: 0.9052 (tp) cc_final: 0.8770 (tp) REVERT: B 201 PHE cc_start: 0.8561 (t80) cc_final: 0.8333 (t80) REVERT: B 429 PHE cc_start: 0.9304 (t80) cc_final: 0.8623 (t80) REVERT: B 1029 MET cc_start: 0.9190 (tpp) cc_final: 0.8422 (tpp) REVERT: B 1050 MET cc_start: 0.8688 (ptt) cc_final: 0.8353 (ptt) REVERT: C 275 PHE cc_start: 0.8314 (m-80) cc_final: 0.7650 (m-80) REVERT: C 342 PHE cc_start: 0.9343 (m-80) cc_final: 0.8973 (m-80) REVERT: C 456 PHE cc_start: 0.8891 (m-10) cc_final: 0.8519 (m-10) REVERT: C 1019 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8281 (tmm-80) REVERT: C 1029 MET cc_start: 0.9229 (tpp) cc_final: 0.8817 (tpp) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.3279 time to fit residues: 99.9746 Evaluate side-chains 114 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.0970 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 24638 Z= 0.160 Angle : 0.505 11.388 33515 Z= 0.258 Chirality : 0.044 0.421 3926 Planarity : 0.004 0.051 4284 Dihedral : 6.199 58.130 4109 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.33 % 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: -0.82 (0.15), residues: 2942 helix: 1.71 (0.22), residues: 637 sheet: -0.46 (0.21), residues: 588 loop : -1.53 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.010 0.001 HIS B1083 PHE 0.029 0.001 PHE A 559 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8299 (t0) cc_final: 0.7954 (t0) REVERT: A 740 MET cc_start: 0.8180 (tmm) cc_final: 0.7935 (tmm) REVERT: A 1050 MET cc_start: 0.8189 (tmm) cc_final: 0.7888 (tmm) REVERT: B 117 LEU cc_start: 0.9049 (tp) cc_final: 0.8781 (tp) REVERT: B 201 PHE cc_start: 0.8577 (t80) cc_final: 0.8352 (t80) REVERT: B 429 PHE cc_start: 0.9287 (t80) cc_final: 0.8756 (t80) REVERT: C 342 PHE cc_start: 0.9338 (m-80) cc_final: 0.8951 (m-80) REVERT: C 387 LEU cc_start: 0.9274 (tp) cc_final: 0.9063 (tt) REVERT: C 456 PHE cc_start: 0.8863 (m-10) cc_final: 0.8520 (m-10) REVERT: C 1019 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.8302 (tmm-80) REVERT: C 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8813 (tpp) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.3194 time to fit residues: 97.3767 Evaluate side-chains 118 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1036 GLN C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24638 Z= 0.194 Angle : 0.509 8.726 33515 Z= 0.262 Chirality : 0.044 0.415 3926 Planarity : 0.004 0.052 4284 Dihedral : 5.755 59.189 4109 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.08 % Allowed : 2.52 % Favored : 97.41 % 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: -0.83 (0.15), residues: 2942 helix: 1.74 (0.22), residues: 635 sheet: -0.47 (0.22), residues: 549 loop : -1.52 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.007 0.001 HIS B1083 PHE 0.025 0.001 PHE C 486 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8208 (t0) cc_final: 0.7948 (t0) REVERT: A 740 MET cc_start: 0.8200 (tmm) cc_final: 0.7938 (tmm) REVERT: A 1050 MET cc_start: 0.8384 (tmm) cc_final: 0.7992 (tmm) REVERT: B 117 LEU cc_start: 0.9085 (tp) cc_final: 0.8829 (tp) REVERT: B 201 PHE cc_start: 0.8595 (t80) cc_final: 0.8386 (t80) REVERT: B 429 PHE cc_start: 0.9288 (t80) cc_final: 0.8758 (t80) REVERT: B 740 MET cc_start: 0.8636 (ttm) cc_final: 0.8170 (ttm) REVERT: C 342 PHE cc_start: 0.9340 (m-80) cc_final: 0.8958 (m-80) REVERT: C 387 LEU cc_start: 0.9281 (tp) cc_final: 0.9054 (tt) REVERT: C 456 PHE cc_start: 0.8927 (m-10) cc_final: 0.8586 (m-10) REVERT: C 1019 ARG cc_start: 0.8575 (tmm-80) cc_final: 0.8290 (tmm-80) REVERT: C 1029 MET cc_start: 0.9251 (tpp) cc_final: 0.8861 (tpp) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.3316 time to fit residues: 100.6238 Evaluate side-chains 117 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24638 Z= 0.357 Angle : 0.627 8.866 33515 Z= 0.322 Chirality : 0.046 0.420 3926 Planarity : 0.004 0.051 4284 Dihedral : 5.914 58.307 4109 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % 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: -1.08 (0.15), residues: 2942 helix: 1.33 (0.21), residues: 631 sheet: -0.53 (0.22), residues: 538 loop : -1.62 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.006 0.001 HIS B1064 PHE 0.025 0.002 PHE A 559 TYR 0.017 0.001 TYR C1067 ARG 0.007 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8240 (t0) cc_final: 0.7914 (t0) REVERT: A 740 MET cc_start: 0.8220 (tmm) cc_final: 0.7939 (tmm) REVERT: A 1050 MET cc_start: 0.8506 (tmm) cc_final: 0.8271 (tmm) REVERT: B 117 LEU cc_start: 0.9114 (tp) cc_final: 0.8885 (tp) REVERT: B 201 PHE cc_start: 0.8725 (t80) cc_final: 0.8522 (t80) REVERT: B 429 PHE cc_start: 0.9331 (t80) cc_final: 0.8674 (t80) REVERT: B 740 MET cc_start: 0.8592 (ttm) cc_final: 0.8327 (ttm) REVERT: C 342 PHE cc_start: 0.9345 (m-80) cc_final: 0.8954 (m-80) REVERT: C 427 ASP cc_start: 0.9271 (p0) cc_final: 0.9017 (p0) REVERT: C 456 PHE cc_start: 0.8959 (m-10) cc_final: 0.8671 (m-10) REVERT: C 1029 MET cc_start: 0.9294 (tpp) cc_final: 0.8916 (tpp) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.3161 time to fit residues: 85.2458 Evaluate side-chains 107 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 388 ASN C 564 GLN C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24638 Z= 0.173 Angle : 0.519 7.150 33515 Z= 0.266 Chirality : 0.044 0.402 3926 Planarity : 0.004 0.050 4284 Dihedral : 5.592 56.538 4109 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 2942 helix: 1.65 (0.22), residues: 635 sheet: -0.48 (0.22), residues: 548 loop : -1.58 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.006 0.001 HIS B1083 PHE 0.023 0.001 PHE C 275 TYR 0.016 0.001 TYR B 369 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8290 (t0) cc_final: 0.7904 (t0) REVERT: A 740 MET cc_start: 0.8189 (tmm) cc_final: 0.7920 (tmm) REVERT: A 1050 MET cc_start: 0.8550 (tmm) cc_final: 0.8280 (tmm) REVERT: B 117 LEU cc_start: 0.9026 (tp) cc_final: 0.8280 (tp) REVERT: B 201 PHE cc_start: 0.8641 (t80) cc_final: 0.8291 (t80) REVERT: B 380 TYR cc_start: 0.9045 (t80) cc_final: 0.8805 (t80) REVERT: C 342 PHE cc_start: 0.9358 (m-80) cc_final: 0.8956 (m-80) REVERT: C 427 ASP cc_start: 0.9216 (p0) cc_final: 0.8955 (p0) REVERT: C 456 PHE cc_start: 0.8944 (m-10) cc_final: 0.8590 (m-10) REVERT: C 1019 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.8339 (tmm-80) REVERT: C 1029 MET cc_start: 0.9321 (tpp) cc_final: 0.8887 (tpp) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.3287 time to fit residues: 95.5174 Evaluate side-chains 114 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 172 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24638 Z= 0.167 Angle : 0.513 6.142 33515 Z= 0.263 Chirality : 0.044 0.396 3926 Planarity : 0.004 0.052 4284 Dihedral : 5.364 58.353 4109 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.08 % Allowed : 0.69 % Favored : 99.24 % 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: -0.81 (0.15), residues: 2942 helix: 1.67 (0.22), residues: 635 sheet: -0.29 (0.22), residues: 550 loop : -1.54 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.021 0.001 PHE B 318 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8246 (t0) cc_final: 0.7868 (t0) REVERT: A 198 ASP cc_start: 0.8597 (m-30) cc_final: 0.8207 (m-30) REVERT: A 740 MET cc_start: 0.8152 (tmm) cc_final: 0.7867 (tmm) REVERT: A 1050 MET cc_start: 0.8557 (tmm) cc_final: 0.8091 (tmm) REVERT: B 117 LEU cc_start: 0.9021 (tp) cc_final: 0.8798 (tp) REVERT: B 429 PHE cc_start: 0.9314 (t80) cc_final: 0.8804 (t80) REVERT: B 740 MET cc_start: 0.8616 (ttt) cc_final: 0.8191 (ttm) REVERT: C 342 PHE cc_start: 0.9346 (m-80) cc_final: 0.8939 (m-80) REVERT: C 369 TYR cc_start: 0.9019 (t80) cc_final: 0.8818 (t80) REVERT: C 427 ASP cc_start: 0.9211 (p0) cc_final: 0.8958 (p0) REVERT: C 456 PHE cc_start: 0.8947 (m-10) cc_final: 0.8606 (m-10) REVERT: C 1019 ARG cc_start: 0.8577 (tmm-80) cc_final: 0.8291 (tmm-80) REVERT: C 1029 MET cc_start: 0.9300 (tpp) cc_final: 0.8830 (tpp) outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.3419 time to fit residues: 101.6236 Evaluate side-chains 126 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 268 optimal weight: 0.0010 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 242 optimal weight: 7.9990 chunk 253 optimal weight: 0.0970 chunk 267 optimal weight: 0.0050 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN C1010 GLN C1036 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24638 Z= 0.134 Angle : 0.500 7.502 33515 Z= 0.255 Chirality : 0.044 0.385 3926 Planarity : 0.004 0.054 4284 Dihedral : 5.145 59.429 4109 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.11 % Allowed : 0.46 % Favored : 99.43 % 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: -0.67 (0.16), residues: 2942 helix: 1.77 (0.22), residues: 639 sheet: -0.23 (0.22), residues: 545 loop : -1.44 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.023 0.001 PHE A 92 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8263 (t0) cc_final: 0.7875 (t0) REVERT: A 740 MET cc_start: 0.8162 (tmm) cc_final: 0.7880 (tmm) REVERT: A 1050 MET cc_start: 0.8573 (tmm) cc_final: 0.8092 (tmm) REVERT: B 117 LEU cc_start: 0.9079 (tp) cc_final: 0.8683 (tp) REVERT: B 201 PHE cc_start: 0.8583 (t80) cc_final: 0.8293 (t80) REVERT: B 429 PHE cc_start: 0.9319 (t80) cc_final: 0.8775 (t80) REVERT: B 740 MET cc_start: 0.8547 (ttt) cc_final: 0.7901 (ttt) REVERT: C 242 LEU cc_start: 0.9015 (tp) cc_final: 0.8542 (pp) REVERT: C 342 PHE cc_start: 0.9361 (m-80) cc_final: 0.8954 (m-80) REVERT: C 369 TYR cc_start: 0.8999 (t80) cc_final: 0.8793 (t80) REVERT: C 427 ASP cc_start: 0.9190 (p0) cc_final: 0.8909 (p0) REVERT: C 456 PHE cc_start: 0.8931 (m-10) cc_final: 0.8453 (m-80) REVERT: C 1019 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8237 (tmm-80) REVERT: C 1029 MET cc_start: 0.9289 (tpp) cc_final: 0.8765 (tpp) outliers start: 3 outliers final: 0 residues processed: 197 average time/residue: 0.3124 time to fit residues: 104.7007 Evaluate side-chains 134 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 2.9990 chunk 283 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24638 Z= 0.236 Angle : 0.538 6.601 33515 Z= 0.277 Chirality : 0.044 0.393 3926 Planarity : 0.004 0.054 4284 Dihedral : 5.225 59.477 4109 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2942 helix: 1.66 (0.22), residues: 630 sheet: -0.21 (0.22), residues: 541 loop : -1.47 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS A1088 PHE 0.022 0.001 PHE A 92 TYR 0.019 0.001 TYR C 695 ARG 0.005 0.000 ARG C1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8254 (t0) cc_final: 0.7891 (t0) REVERT: A 740 MET cc_start: 0.8174 (tmm) cc_final: 0.7901 (tmm) REVERT: A 1050 MET cc_start: 0.8624 (tmm) cc_final: 0.8158 (tmm) REVERT: B 117 LEU cc_start: 0.9068 (tp) cc_final: 0.8783 (tp) REVERT: B 429 PHE cc_start: 0.9362 (t80) cc_final: 0.8804 (t80) REVERT: B 740 MET cc_start: 0.8591 (ttt) cc_final: 0.7986 (ttt) REVERT: C 342 PHE cc_start: 0.9362 (m-80) cc_final: 0.8967 (m-80) REVERT: C 456 PHE cc_start: 0.8974 (m-10) cc_final: 0.8664 (m-10) REVERT: C 1029 MET cc_start: 0.9279 (tpp) cc_final: 0.8838 (tpp) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.3037 time to fit residues: 89.3367 Evaluate side-chains 118 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 907 ASN A1083 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 853 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.083369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055503 restraints weight = 91503.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058068 restraints weight = 54848.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058693 restraints weight = 31089.346| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24638 Z= 0.312 Angle : 0.595 9.257 33515 Z= 0.307 Chirality : 0.045 0.396 3926 Planarity : 0.004 0.056 4284 Dihedral : 5.501 58.657 4109 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % 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: -0.94 (0.15), residues: 2942 helix: 1.42 (0.22), residues: 628 sheet: -0.36 (0.22), residues: 547 loop : -1.55 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.005 0.001 HIS A1088 PHE 0.027 0.002 PHE A 559 TYR 0.022 0.001 TYR C 873 ARG 0.006 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.28 seconds wall clock time: 71 minutes 58.57 seconds (4318.57 seconds total)