Starting phenix.real_space_refine on Mon Aug 25 08:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy0_60551/08_2025/8zy0_60551.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 132 5.16 5 C 16899 2.51 5 N 4313 2.21 5 O 5267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26611 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8509 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 47, 'TRANS': 1044} Chain breaks: 2 Chain: "B" Number of atoms: 8509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8509 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 47, 'TRANS': 1044} Chain breaks: 2 Chain: "C" Number of atoms: 8505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8505 Classifications: {'peptide': 1092} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 281 Unusual residues: {'BLA': 1, 'NAG': 17} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 281 Unusual residues: {'BLA': 1, 'NAG': 17} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 281 Unusual residues: {'BLA': 1, 'NAG': 17} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 6.68, per 1000 atoms: 0.25 Number of scatterers: 26611 At special positions: 0 Unit cell: (141.255, 150.015, 168.63, 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 132 16.00 O 5267 8.00 N 4313 7.00 C 16899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 723 " - pdb=" SG CYS A 745 " distance=2.02 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A1017 " - pdb=" SG CYS A1028 " distance=2.02 Simple disulfide: pdb=" SG CYS A1067 " - pdb=" SG CYS A1111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 514 " distance=2.04 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 723 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 734 " distance=2.03 Simple disulfide: pdb=" SG CYS B1017 " - pdb=" SG CYS B1028 " distance=2.02 Simple disulfide: pdb=" SG CYS B1067 " - pdb=" SG CYS B1111 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 514 " distance=2.00 Simple disulfide: pdb=" SG CYS C 469 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 640 " distance=2.02 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 723 " - pdb=" SG CYS C 745 " distance=2.02 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 734 " distance=2.03 Simple disulfide: pdb=" SG CYS C1017 " - pdb=" SG CYS C1028 " distance=2.02 Simple disulfide: pdb=" SG CYS C1067 " - pdb=" SG CYS C1111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1201 " - " ASN A 321 " " NAG A1202 " - " ASN A 24 " " NAG A1203 " - " ASN A 65 " " NAG A1204 " - " ASN A 125 " " NAG A1205 " - " ASN A 159 " " NAG A1206 " - " ASN A 162 " " NAG A1207 " - " ASN A 272 " " NAG A1208 " - " ASN A 333 " " NAG A1209 " - " ASN A 360 " " NAG A1210 " - " ASN A 592 " " NAG A1211 " - " ASN A 605 " " NAG A1212 " - " ASN A 648 " " NAG A1213 " - " ASN A 702 " " NAG A1214 " - " ASN A 786 " " NAG A1215 " - " ASN A1059 " " NAG A1216 " - " ASN A1083 " " NAG A1217 " - " ASN A1119 " " NAG B1201 " - " ASN B 321 " " NAG B1202 " - " ASN B 24 " " NAG B1203 " - " ASN B 65 " " NAG B1204 " - " ASN B 125 " " NAG B1205 " - " ASN B 159 " " NAG B1206 " - " ASN B 272 " " NAG B1207 " - " ASN B 333 " " NAG B1208 " - " ASN B 360 " " NAG B1209 " - " ASN B 592 " " NAG B1210 " - " ASN B 605 " " NAG B1211 " - " ASN B 648 " " NAG B1212 " - " ASN B 702 " " NAG B1213 " - " ASN B 786 " " NAG B1214 " - " ASN B1059 " " NAG B1215 " - " ASN B1083 " " NAG B1216 " - " ASN B1119 " " NAG B1218 " - " ASN B 162 " " NAG C1201 " - " ASN C 321 " " NAG C1202 " - " ASN C 24 " " NAG C1203 " - " ASN C 125 " " NAG C1204 " - " ASN C 159 " " NAG C1205 " - " ASN C 162 " " NAG C1206 " - " ASN C 272 " " NAG C1207 " - " ASN C 333 " " NAG C1208 " - " ASN C 360 " " NAG C1209 " - " ASN C 592 " " NAG C1210 " - " ASN C 605 " " NAG C1211 " - " ASN C 648 " " NAG C1212 " - " ASN C 702 " " NAG C1213 " - " ASN C 786 " " NAG C1214 " - " ASN C1059 " " NAG C1215 " - " ASN C1083 " " NAG C1216 " - " ASN C1119 " " NAG C1218 " - " ASN C 65 " " NAG D 1 " - " ASN A 115 " " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 115 " " NAG G 1 " - " ASN B 230 " " NAG H 1 " - " ASN C 115 " " NAG I 1 " - " ASN C 230 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 46 sheets defined 23.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.671A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.709A pdb=" N VAL A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 360 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.867A pdb=" N LEU A 378 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 379' Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.504A pdb=" N VAL A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 619 through 626 removed outlier: 4.075A pdb=" N VAL A 624 " --> pdb=" O ASP A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 731 through 740 removed outlier: 3.943A pdb=" N ASN A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 768 removed outlier: 3.527A pdb=" N ASP A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 767 " --> pdb=" O THR A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 807 Processing helix chain 'A' and resid 833 through 840 removed outlier: 3.764A pdb=" N ALA A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 867 removed outlier: 4.271A pdb=" N GLY A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 882 through 895 Processing helix chain 'A' and resid 904 through 925 removed outlier: 3.539A pdb=" N ASN A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 949 removed outlier: 4.077A pdb=" N VAL A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 941 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 953 removed outlier: 3.518A pdb=" N SER A 953 " --> pdb=" O GLN A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'A' and resid 970 through 1018 removed outlier: 3.988A pdb=" N GLU A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN A 977 " --> pdb=" O GLU A 973 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 981 " --> pdb=" O GLN A 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.530A pdb=" N PHE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.839A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.815A pdb=" N VAL B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 360 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.903A pdb=" N LEU B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 379 " --> pdb=" O THR B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 608 through 614 removed outlier: 3.605A pdb=" N MET B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 removed outlier: 3.615A pdb=" N VAL B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 619 through 626 removed outlier: 4.134A pdb=" N VAL B 624 " --> pdb=" O ASP B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 743 through 767 removed outlier: 3.582A pdb=" N GLN B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 763 " --> pdb=" O GLN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 807 Processing helix chain 'B' and resid 833 through 840 removed outlier: 3.697A pdb=" N ALA B 837 " --> pdb=" O ASP B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 867 removed outlier: 4.326A pdb=" N GLY B 865 " --> pdb=" O ALA B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 removed outlier: 3.502A pdb=" N GLY B 874 " --> pdb=" O TYR B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 895 Processing helix chain 'B' and resid 904 through 925 removed outlier: 3.917A pdb=" N ILE B 919 " --> pdb=" O ALA B 915 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 949 removed outlier: 4.304A pdb=" N VAL B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN B 940 " --> pdb=" O VAL B 936 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 941 " --> pdb=" O ILE B 937 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 953 removed outlier: 3.628A pdb=" N SER B 953 " --> pdb=" O GLN B 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 953' Processing helix chain 'B' and resid 961 through 969 removed outlier: 3.533A pdb=" N ARG B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 1018 removed outlier: 4.053A pdb=" N ARG B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 981 " --> pdb=" O GLN B 977 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 992 " --> pdb=" O SER B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.677A pdb=" N TRP C 343 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.810A pdb=" N VAL C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 360 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.550A pdb=" N MET C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 removed outlier: 3.514A pdb=" N VAL C 618 " --> pdb=" O VAL C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 619 through 626 removed outlier: 4.163A pdb=" N VAL C 624 " --> pdb=" O ASP C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 727 Processing helix chain 'C' and resid 731 through 739 removed outlier: 3.849A pdb=" N SER C 735 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 737 " --> pdb=" O GLU C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 767 removed outlier: 3.707A pdb=" N GLN C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 763 " --> pdb=" O GLN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 807 Processing helix chain 'C' and resid 833 through 840 removed outlier: 3.684A pdb=" N ALA C 837 " --> pdb=" O ASP C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 867 removed outlier: 4.284A pdb=" N GLY C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'C' and resid 882 through 895 Processing helix chain 'C' and resid 898 through 903 removed outlier: 3.763A pdb=" N TYR C 902 " --> pdb=" O GLN C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 925 removed outlier: 3.968A pdb=" N ILE C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP C 921 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 949 removed outlier: 4.416A pdb=" N VAL C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C 940 " --> pdb=" O VAL C 936 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 941 " --> pdb=" O ILE C 937 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 949 " --> pdb=" O ASN C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 953 removed outlier: 3.619A pdb=" N SER C 953 " --> pdb=" O GLN C 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 950 through 953' Processing helix chain 'C' and resid 961 through 969 Processing helix chain 'C' and resid 970 through 1018 removed outlier: 4.320A pdb=" N GLU C 975 " --> pdb=" O LYS C 971 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN C 977 " --> pdb=" O GLU C 973 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 981 " --> pdb=" O GLN C 977 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.546A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 65 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS A 259 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 67 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 189 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU A 197 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 199 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.413A pdb=" N ASP A 277 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 170 removed outlier: 7.015A pdb=" N ALA A 145 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER A 154 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N MET A 143 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 156 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A 141 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 158 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N CYS A 139 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 160 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR A 137 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN A 162 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 135 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR A 164 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL A 133 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 166 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 131 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 168 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 129 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 110 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 170 removed outlier: 7.015A pdb=" N ALA A 145 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER A 154 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N MET A 143 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 156 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A 141 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 158 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N CYS A 139 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 160 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR A 137 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN A 162 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 135 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR A 164 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL A 133 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 166 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 131 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 168 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 129 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 238 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305 removed outlier: 4.674A pdb=" N VAL A 584 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 601 " --> pdb=" O CYS A 640 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 640 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 639 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.537A pdb=" N SER A 577 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 563 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 564 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.846A pdb=" N GLU A 344 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 390 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 348 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 386 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 385 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 352 removed outlier: 6.411A pdb=" N CYS A 351 " --> pdb=" O CYS A 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 513 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB2, first strand: chain 'A' and resid 645 through 646 removed outlier: 6.157A pdb=" N ILE A 645 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 681 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 696 through 699 removed outlier: 4.555A pdb=" N THR A1061 " --> pdb=" O MET A1082 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A1082 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A1063 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A1080 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 713 removed outlier: 3.521A pdb=" N SER A 706 " --> pdb=" O THR A1051 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 710 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 712 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR A1052 " --> pdb=" O HIS A1033 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS A1033 " --> pdb=" O TYR A1052 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 720 removed outlier: 4.383A pdb=" N LYS A 718 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1105 through 1110 removed outlier: 3.508A pdb=" N PHE A1074 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A1108 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA A1072 " --> pdb=" O SER A1108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.638A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASN B 65 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS B 259 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 189 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 197 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 224 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 199 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR B 203 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL B 218 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG B 38 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N LEU B 219 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE B 40 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.783A pdb=" N GLU B 268 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP B 277 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 170 removed outlier: 7.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ASP B 141 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ASN B 159 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS B 139 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 161 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS B 163 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN B 135 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 133 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 110 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 151 through 170 removed outlier: 7.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ASP B 141 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ASN B 159 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS B 139 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 161 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS B 163 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN B 135 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 133 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET B 238 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 301 through 305 removed outlier: 4.682A pdb=" N VAL B 584 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.593A pdb=" N SER B 577 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP B 563 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 564 " --> pdb=" O GLY B 555 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.838A pdb=" N GLU B 344 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 390 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 348 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 386 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AC6, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC7, first strand: chain 'B' and resid 645 through 646 removed outlier: 6.195A pdb=" N ILE B 645 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 681 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 687 through 688 Processing sheet with id=AC9, first strand: chain 'B' and resid 696 through 698 removed outlier: 4.442A pdb=" N THR B1061 " --> pdb=" O MET B1082 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B1082 " --> pdb=" O THR B1061 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B1063 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B1080 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 703 through 713 removed outlier: 3.611A pdb=" N LEU B 712 " --> pdb=" O VAL B1045 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B1052 " --> pdb=" O HIS B1033 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS B1033 " --> pdb=" O TYR B1052 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 720 removed outlier: 4.270A pdb=" N LYS B 718 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1105 through 1110 removed outlier: 3.686A pdb=" N SER B1108 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA B1072 " --> pdb=" O SER B1108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.728A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASN C 65 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N HIS C 259 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 189 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 197 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS C 224 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 199 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C 203 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL C 218 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N ARG C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 11.366A pdb=" N PHE C 216 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG C 38 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU C 219 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE C 40 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.374A pdb=" N ASP C 277 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 150 through 161 removed outlier: 6.991A pdb=" N ALA C 145 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER C 154 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET C 143 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 156 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP C 141 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU C 158 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N CYS C 139 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA C 160 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR C 137 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 110 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 166 through 170 removed outlier: 10.131A pdb=" N MET C 238 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU C 240 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 144 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 301 through 305 removed outlier: 4.798A pdb=" N VAL C 584 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 601 " --> pdb=" O CYS C 640 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS C 640 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 639 " --> pdb=" O THR C 636 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.640A pdb=" N SER C 577 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 564 " --> pdb=" O GLY C 555 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.761A pdb=" N GLU C 344 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 386 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 382 through 383 removed outlier: 3.575A pdb=" N VAL C 513 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 441 through 443 Processing sheet with id=AE4, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AE5, first strand: chain 'C' and resid 645 through 646 removed outlier: 6.221A pdb=" N ILE C 645 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR C 681 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 696 through 698 Processing sheet with id=AE7, first strand: chain 'C' and resid 703 through 713 removed outlier: 3.627A pdb=" N SER C 706 " --> pdb=" O THR C1051 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C1052 " --> pdb=" O HIS C1033 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS C1033 " --> pdb=" O TYR C1052 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 720 removed outlier: 4.402A pdb=" N LYS C 718 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1105 through 1107 Processing sheet with id=AF1, first strand: chain 'C' and resid 1079 through 1082 893 hydrogen bonds defined for protein. 2391 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: 7.12 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7559 1.33 - 1.46: 7716 1.46 - 1.59: 11759 1.59 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 27211 Sorted by residual: bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.490 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1D BLA B1217 " pdb=" CHD BLA B1217 " ideal model delta sigma weight residual 1.440 1.363 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1D BLA C1217 " pdb=" CHD BLA C1217 " ideal model delta sigma weight residual 1.440 1.363 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.493 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1D BLA A1218 " pdb=" CHD BLA A1218 " ideal model delta sigma weight residual 1.440 1.368 0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 27206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 36022 2.06 - 4.11: 858 4.11 - 6.17: 100 6.17 - 8.22: 42 8.22 - 10.28: 6 Bond angle restraints: 37028 Sorted by residual: angle pdb=" N PHE B1027 " pdb=" CA PHE B1027 " pdb=" C PHE B1027 " ideal model delta sigma weight residual 113.41 107.53 5.88 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N ASP B 396 " pdb=" CA ASP B 396 " pdb=" C ASP B 396 " ideal model delta sigma weight residual 113.02 107.66 5.36 1.20e+00 6.94e-01 1.99e+01 angle pdb=" CA ASP A 730 " pdb=" CB ASP A 730 " pdb=" CG ASP A 730 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" C PRO A 285 " pdb=" N LEU A 286 " pdb=" CA LEU A 286 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N GLN B 637 " pdb=" CA GLN B 637 " pdb=" C GLN B 637 " ideal model delta sigma weight residual 113.38 108.63 4.75 1.23e+00 6.61e-01 1.49e+01 ... (remaining 37023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 16217 24.21 - 48.42: 665 48.42 - 72.62: 124 72.62 - 96.83: 36 96.83 - 121.04: 16 Dihedral angle restraints: 17058 sinusoidal: 7512 harmonic: 9546 Sorted by residual: dihedral pdb=" CB CYS B 728 " pdb=" SG CYS B 728 " pdb=" SG CYS B 734 " pdb=" CB CYS B 734 " ideal model delta sinusoidal sigma weight residual -86.00 -168.84 82.84 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 640 " pdb=" CB CYS B 640 " ideal model delta sinusoidal sigma weight residual 93.00 19.62 73.38 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS C 527 " pdb=" SG CYS C 527 " pdb=" SG CYS C 579 " pdb=" CB CYS C 579 " ideal model delta sinusoidal sigma weight residual -86.00 -30.93 -55.07 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 17055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3546 0.066 - 0.132: 761 0.132 - 0.198: 45 0.198 - 0.264: 5 0.264 - 0.330: 7 Chirality restraints: 4364 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C2 NAG H 1 " pdb=" C1 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" N2 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4361 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1217 " 0.029 2.00e-02 2.50e+03 1.97e-01 9.67e+02 pdb=" C1D BLA B1217 " -0.354 2.00e-02 2.50e+03 pdb=" C2C BLA B1217 " -0.020 2.00e-02 2.50e+03 pdb=" C3C BLA B1217 " 0.045 2.00e-02 2.50e+03 pdb=" C4C BLA B1217 " 0.171 2.00e-02 2.50e+03 pdb=" CAC BLA B1217 " -0.028 2.00e-02 2.50e+03 pdb=" CHD BLA B1217 " 0.067 2.00e-02 2.50e+03 pdb=" CMC BLA B1217 " -0.125 2.00e-02 2.50e+03 pdb=" NC BLA B1217 " 0.412 2.00e-02 2.50e+03 pdb=" OC BLA B1217 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1218 " -0.427 2.00e-02 2.50e+03 1.92e-01 9.19e+02 pdb=" C1A BLA A1218 " 0.286 2.00e-02 2.50e+03 pdb=" C1D BLA A1218 " -0.043 2.00e-02 2.50e+03 pdb=" C2D BLA A1218 " 0.004 2.00e-02 2.50e+03 pdb=" C3D BLA A1218 " -0.041 2.00e-02 2.50e+03 pdb=" C4D BLA A1218 " -0.168 2.00e-02 2.50e+03 pdb=" CAD BLA A1218 " 0.065 2.00e-02 2.50e+03 pdb=" CHA BLA A1218 " -0.002 2.00e-02 2.50e+03 pdb=" CHD BLA A1218 " 0.247 2.00e-02 2.50e+03 pdb=" CMD BLA A1218 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1218 " -0.011 2.00e-02 2.50e+03 1.77e-01 7.83e+02 pdb=" C1D BLA A1218 " 0.244 2.00e-02 2.50e+03 pdb=" C2C BLA A1218 " -0.006 2.00e-02 2.50e+03 pdb=" C3C BLA A1218 " -0.015 2.00e-02 2.50e+03 pdb=" C4C BLA A1218 " -0.139 2.00e-02 2.50e+03 pdb=" CAC BLA A1218 " 0.090 2.00e-02 2.50e+03 pdb=" CHD BLA A1218 " -0.029 2.00e-02 2.50e+03 pdb=" CMC BLA A1218 " 0.015 2.00e-02 2.50e+03 pdb=" NC BLA A1218 " -0.401 2.00e-02 2.50e+03 pdb=" OC BLA A1218 " 0.252 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4600 2.77 - 3.30: 23044 3.30 - 3.84: 41769 3.84 - 4.37: 47691 4.37 - 4.90: 86440 Nonbonded interactions: 203544 Sorted by model distance: nonbonded pdb=" OE2 GLU B 268 " pdb=" OG1 THR B 276 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 362 " pdb=" OH TYR C 494 " model vdw 2.294 3.040 nonbonded pdb=" OG SER B 242 " pdb=" OG1 THR B 245 " model vdw 2.296 3.040 nonbonded pdb=" O LEU A 862 " pdb=" OG1 THR A 866 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU C 268 " pdb=" OG1 THR C 276 " model vdw 2.304 3.040 ... (remaining 203539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 794 or (resid 795 and (name N or name CA or nam \ e C or name O or name CB )) or resid 796 through 1216)) selection = (chain 'B' and (resid 17 through 794 or (resid 795 and (name N or name CA or nam \ e C or name O or name CB )) or resid 796 through 1216)) selection = (chain 'C' and resid 17 through 1216) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.005 0.091 27323 Z= 0.245 Angle : 0.759 10.277 37322 Z= 0.382 Chirality : 0.052 0.330 4364 Planarity : 0.008 0.197 4692 Dihedral : 13.973 121.038 10812 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.13), residues: 3258 helix: -1.14 (0.18), residues: 687 sheet: 0.36 (0.20), residues: 708 loop : -1.85 (0.12), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.018 0.001 TYR B 484 PHE 0.035 0.001 PHE B1106 TRP 0.007 0.001 TRP B 622 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00472 (27211) covalent geometry : angle 0.74399 (37028) SS BOND : bond 0.00752 ( 42) SS BOND : angle 1.75970 ( 84) hydrogen bonds : bond 0.23861 ( 882) hydrogen bonds : angle 8.29862 ( 2391) link_ALPHA1-2 : bond 0.00248 ( 1) link_ALPHA1-2 : angle 2.24433 ( 3) link_ALPHA1-3 : bond 0.01972 ( 3) link_ALPHA1-3 : angle 3.80025 ( 9) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 1.98431 ( 27) link_NAG-ASN : bond 0.00272 ( 57) link_NAG-ASN : angle 1.65635 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 765 ASP cc_start: 0.7547 (m-30) cc_final: 0.7323 (m-30) REVERT: A 935 ASP cc_start: 0.7625 (m-30) cc_final: 0.7342 (m-30) REVERT: B 854 MET cc_start: 0.8601 (mtp) cc_final: 0.8270 (mtp) REVERT: B 1082 MET cc_start: 0.7330 (ptm) cc_final: 0.7118 (ptm) outliers start: 2 outliers final: 1 residues processed: 321 average time/residue: 0.7263 time to fit residues: 269.1827 Evaluate side-chains 190 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 533 ASN A 617 GLN A 886 GLN B 553 GLN B 886 GLN B 907 GLN B 911 GLN C 617 GLN C 920 GLN C1091 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096110 restraints weight = 35632.455| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.41 r_work: 0.2889 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27323 Z= 0.144 Angle : 0.622 9.680 37322 Z= 0.312 Chirality : 0.046 0.278 4364 Planarity : 0.004 0.054 4692 Dihedral : 10.668 105.087 5079 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.44 % Allowed : 8.23 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.14), residues: 3258 helix: -0.55 (0.19), residues: 732 sheet: 0.41 (0.20), residues: 729 loop : -1.79 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1092 TYR 0.022 0.001 TYR B1052 PHE 0.025 0.001 PHE C1106 TRP 0.008 0.001 TRP C 427 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00331 (27211) covalent geometry : angle 0.60589 (37028) SS BOND : bond 0.00504 ( 42) SS BOND : angle 1.52489 ( 84) hydrogen bonds : bond 0.05364 ( 882) hydrogen bonds : angle 6.07299 ( 2391) link_ALPHA1-2 : bond 0.00556 ( 1) link_ALPHA1-2 : angle 1.66275 ( 3) link_ALPHA1-3 : bond 0.03064 ( 3) link_ALPHA1-3 : angle 3.93541 ( 9) link_BETA1-4 : bond 0.00684 ( 9) link_BETA1-4 : angle 2.02146 ( 27) link_NAG-ASN : bond 0.00274 ( 57) link_NAG-ASN : angle 1.53493 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8352 (p) cc_final: 0.8076 (m) REVERT: A 765 ASP cc_start: 0.8507 (m-30) cc_final: 0.8298 (m-30) REVERT: A 935 ASP cc_start: 0.8181 (m-30) cc_final: 0.7916 (m-30) REVERT: A 995 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: B 854 MET cc_start: 0.9020 (mtp) cc_final: 0.8766 (mtp) REVERT: B 1071 LYS cc_start: 0.8454 (pttm) cc_final: 0.8170 (pttp) REVERT: B 1115 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 271 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7263 (pp20) REVERT: C 761 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8110 (ttm170) REVERT: C 1115 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8443 (mm) outliers start: 41 outliers final: 7 residues processed: 231 average time/residue: 0.7398 time to fit residues: 197.1732 Evaluate side-chains 188 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 54 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 617 GLN A 910 ASN A 934 GLN C 920 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091526 restraints weight = 35655.594| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.38 r_work: 0.2802 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27323 Z= 0.196 Angle : 0.680 12.152 37322 Z= 0.339 Chirality : 0.049 0.298 4364 Planarity : 0.004 0.043 4692 Dihedral : 9.402 94.789 5077 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.42 % Allowed : 11.00 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.14), residues: 3258 helix: -0.26 (0.19), residues: 705 sheet: 0.32 (0.20), residues: 747 loop : -1.70 (0.12), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1092 TYR 0.023 0.002 TYR B1052 PHE 0.034 0.002 PHE A 337 TRP 0.008 0.001 TRP B 427 HIS 0.005 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00476 (27211) covalent geometry : angle 0.65950 (37028) SS BOND : bond 0.00718 ( 42) SS BOND : angle 1.88863 ( 84) hydrogen bonds : bond 0.05938 ( 882) hydrogen bonds : angle 5.68104 ( 2391) link_ALPHA1-2 : bond 0.00585 ( 1) link_ALPHA1-2 : angle 2.33748 ( 3) link_ALPHA1-3 : bond 0.02801 ( 3) link_ALPHA1-3 : angle 5.01963 ( 9) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 2.21769 ( 27) link_NAG-ASN : bond 0.00337 ( 57) link_NAG-ASN : angle 1.66514 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 1.055 Fit side-chains REVERT: A 208 VAL cc_start: 0.8409 (p) cc_final: 0.8097 (m) REVERT: A 765 ASP cc_start: 0.8630 (m-30) cc_final: 0.8383 (m-30) REVERT: A 935 ASP cc_start: 0.8317 (m-30) cc_final: 0.8053 (m-30) REVERT: A 1014 MET cc_start: 0.9020 (tpp) cc_final: 0.8732 (tpp) REVERT: B 296 LEU cc_start: 0.8996 (mm) cc_final: 0.8772 (mm) REVERT: B 637 GLN cc_start: 0.8597 (mm-40) cc_final: 0.7869 (tm-30) REVERT: B 1115 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 99 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8648 (pm20) REVERT: C 271 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: C 616 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: C 761 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8032 (ttm170) REVERT: C 885 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (mtm) REVERT: C 1115 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8508 (mm) outliers start: 69 outliers final: 25 residues processed: 259 average time/residue: 0.7058 time to fit residues: 212.2079 Evaluate side-chains 208 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 640 CYS Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 269 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 617 GLN A 934 GLN C 304 GLN C 920 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094061 restraints weight = 35453.746| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.35 r_work: 0.2834 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27323 Z= 0.122 Angle : 0.598 11.320 37322 Z= 0.296 Chirality : 0.045 0.278 4364 Planarity : 0.004 0.048 4692 Dihedral : 8.719 91.608 5077 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.38 % Allowed : 13.24 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.14), residues: 3258 helix: 0.00 (0.20), residues: 711 sheet: 0.40 (0.20), residues: 735 loop : -1.63 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1092 TYR 0.018 0.001 TYR B1052 PHE 0.017 0.001 PHE C1106 TRP 0.008 0.001 TRP B 427 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00274 (27211) covalent geometry : angle 0.57967 (37028) SS BOND : bond 0.00446 ( 42) SS BOND : angle 1.43651 ( 84) hydrogen bonds : bond 0.04836 ( 882) hydrogen bonds : angle 5.50952 ( 2391) link_ALPHA1-2 : bond 0.00653 ( 1) link_ALPHA1-2 : angle 1.90972 ( 3) link_ALPHA1-3 : bond 0.02853 ( 3) link_ALPHA1-3 : angle 4.74692 ( 9) link_BETA1-4 : bond 0.00447 ( 9) link_BETA1-4 : angle 2.01511 ( 27) link_NAG-ASN : bond 0.00213 ( 57) link_NAG-ASN : angle 1.50335 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 201 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8457 (p) cc_final: 0.8201 (m) REVERT: A 268 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: A 557 ASP cc_start: 0.8150 (t0) cc_final: 0.7949 (t0) REVERT: A 765 ASP cc_start: 0.8543 (m-30) cc_final: 0.8274 (m-30) REVERT: A 935 ASP cc_start: 0.8237 (m-30) cc_final: 0.7947 (m-30) REVERT: A 995 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: A 1014 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8660 (tpp) REVERT: B 271 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: B 296 LEU cc_start: 0.8988 (mm) cc_final: 0.8746 (mm) REVERT: B 547 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8156 (mtmm) REVERT: B 1115 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8803 (mm) REVERT: C 271 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: C 761 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8176 (ttm170) REVERT: C 885 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8857 (mtm) outliers start: 68 outliers final: 23 residues processed: 251 average time/residue: 0.6907 time to fit residues: 201.7017 Evaluate side-chains 205 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1086 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 252 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 313 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 181 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 911 GLN B1104 ASN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.093930 restraints weight = 35410.350| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.35 r_work: 0.2848 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 27323 Z= 0.124 Angle : 0.602 12.974 37322 Z= 0.297 Chirality : 0.045 0.297 4364 Planarity : 0.004 0.058 4692 Dihedral : 8.313 88.765 5077 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.59 % Allowed : 14.05 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3258 helix: 0.20 (0.20), residues: 708 sheet: 0.41 (0.20), residues: 726 loop : -1.56 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1092 TYR 0.020 0.001 TYR B1052 PHE 0.016 0.001 PHE B 227 TRP 0.008 0.001 TRP B 427 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00287 (27211) covalent geometry : angle 0.58154 (37028) SS BOND : bond 0.00518 ( 42) SS BOND : angle 1.94185 ( 84) hydrogen bonds : bond 0.04659 ( 882) hydrogen bonds : angle 5.41319 ( 2391) link_ALPHA1-2 : bond 0.00610 ( 1) link_ALPHA1-2 : angle 1.94890 ( 3) link_ALPHA1-3 : bond 0.02913 ( 3) link_ALPHA1-3 : angle 4.77918 ( 9) link_BETA1-4 : bond 0.00463 ( 9) link_BETA1-4 : angle 1.98752 ( 27) link_NAG-ASN : bond 0.00219 ( 57) link_NAG-ASN : angle 1.47767 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 672 MET cc_start: 0.5498 (tpt) cc_final: 0.5231 (tpp) REVERT: A 765 ASP cc_start: 0.8553 (m-30) cc_final: 0.8303 (m-30) REVERT: A 894 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7407 (tp) REVERT: A 935 ASP cc_start: 0.8300 (m-30) cc_final: 0.8010 (m-30) REVERT: A 995 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: A 1014 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8703 (tpp) REVERT: B 271 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7359 (pp20) REVERT: B 296 LEU cc_start: 0.8982 (mm) cc_final: 0.8742 (mm) REVERT: B 324 ASN cc_start: 0.8259 (p0) cc_final: 0.7917 (p0) REVERT: B 424 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8930 (t) REVERT: B 547 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8120 (mtmm) REVERT: B 637 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8046 (tm-30) REVERT: B 1115 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8770 (mm) REVERT: C 271 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: C 761 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8167 (ttm170) REVERT: C 885 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8864 (mtm) outliers start: 74 outliers final: 34 residues processed: 241 average time/residue: 0.6949 time to fit residues: 194.9868 Evaluate side-chains 217 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1082 MET Chi-restraints excluded: chain C residue 1086 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 153 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 265 optimal weight: 0.1980 chunk 287 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 219 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A1104 ASN B 617 GLN B 789 GLN B 920 GLN C 789 GLN C 920 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096336 restraints weight = 35377.474| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.34 r_work: 0.2882 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27323 Z= 0.104 Angle : 0.568 11.276 37322 Z= 0.279 Chirality : 0.044 0.272 4364 Planarity : 0.003 0.063 4692 Dihedral : 7.809 84.657 5077 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3258 helix: 0.20 (0.20), residues: 732 sheet: 0.53 (0.20), residues: 714 loop : -1.53 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B1092 TYR 0.017 0.001 TYR B1052 PHE 0.015 0.001 PHE B 227 TRP 0.007 0.001 TRP B 427 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00225 (27211) covalent geometry : angle 0.54960 (37028) SS BOND : bond 0.00480 ( 42) SS BOND : angle 1.56408 ( 84) hydrogen bonds : bond 0.04137 ( 882) hydrogen bonds : angle 5.27382 ( 2391) link_ALPHA1-2 : bond 0.00588 ( 1) link_ALPHA1-2 : angle 2.01111 ( 3) link_ALPHA1-3 : bond 0.03112 ( 3) link_ALPHA1-3 : angle 4.85653 ( 9) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.85013 ( 27) link_NAG-ASN : bond 0.00206 ( 57) link_NAG-ASN : angle 1.39521 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8413 (tt0) REVERT: A 557 ASP cc_start: 0.8038 (t0) cc_final: 0.7774 (t0) REVERT: A 894 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7268 (tp) REVERT: A 935 ASP cc_start: 0.8288 (m-30) cc_final: 0.7992 (m-30) REVERT: A 995 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: A 1014 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8650 (tpp) REVERT: B 271 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: B 296 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8740 (mm) REVERT: B 424 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8906 (t) REVERT: B 547 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8173 (mtmm) REVERT: C 315 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: C 761 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8057 (ttm170) REVERT: C 885 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (mtm) outliers start: 67 outliers final: 25 residues processed: 248 average time/residue: 0.5831 time to fit residues: 168.9914 Evaluate side-chains 211 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1082 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 995 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 174 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 192 ASN B1104 ASN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094876 restraints weight = 35371.755| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.35 r_work: 0.2830 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27323 Z= 0.128 Angle : 0.591 11.486 37322 Z= 0.291 Chirality : 0.045 0.280 4364 Planarity : 0.004 0.066 4692 Dihedral : 7.650 83.185 5077 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 15.31 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3258 helix: 0.35 (0.20), residues: 711 sheet: 0.51 (0.20), residues: 714 loop : -1.54 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1092 TYR 0.019 0.001 TYR B1052 PHE 0.017 0.001 PHE B 227 TRP 0.007 0.001 TRP B 427 HIS 0.003 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00298 (27211) covalent geometry : angle 0.57259 (37028) SS BOND : bond 0.00559 ( 42) SS BOND : angle 1.63691 ( 84) hydrogen bonds : bond 0.04482 ( 882) hydrogen bonds : angle 5.24206 ( 2391) link_ALPHA1-2 : bond 0.00471 ( 1) link_ALPHA1-2 : angle 1.95224 ( 3) link_ALPHA1-3 : bond 0.03249 ( 3) link_ALPHA1-3 : angle 5.06772 ( 9) link_BETA1-4 : bond 0.00466 ( 9) link_BETA1-4 : angle 1.86421 ( 27) link_NAG-ASN : bond 0.00213 ( 57) link_NAG-ASN : angle 1.43756 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 185 time to evaluate : 0.989 Fit side-chains REVERT: A 557 ASP cc_start: 0.8107 (t0) cc_final: 0.7889 (t0) REVERT: A 672 MET cc_start: 0.5658 (tpt) cc_final: 0.5405 (tpp) REVERT: A 688 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: A 894 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7275 (tp) REVERT: A 935 ASP cc_start: 0.8271 (m-30) cc_final: 0.7987 (m-30) REVERT: A 995 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: A 1014 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8708 (tpp) REVERT: A 1071 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8385 (pttt) REVERT: B 271 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7407 (pp20) REVERT: B 296 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8757 (mm) REVERT: B 324 ASN cc_start: 0.8139 (p0) cc_final: 0.7857 (p0) REVERT: B 424 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 547 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8147 (mtmm) REVERT: B 899 ASN cc_start: 0.8328 (t0) cc_final: 0.8111 (t0) REVERT: C 315 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: C 616 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 761 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (ttm170) REVERT: C 885 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8876 (mtm) REVERT: C 990 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: C 995 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: C 1115 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8505 (mm) outliers start: 79 outliers final: 34 residues processed: 243 average time/residue: 0.6544 time to fit residues: 184.0005 Evaluate side-chains 227 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1082 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1082 MET Chi-restraints excluded: chain C residue 1086 HIS Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 39 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 637 GLN B 192 ASN B 920 GLN C 789 GLN C 920 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.092762 restraints weight = 35638.116| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.38 r_work: 0.2799 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27323 Z= 0.148 Angle : 0.622 11.835 37322 Z= 0.307 Chirality : 0.046 0.282 4364 Planarity : 0.004 0.067 4692 Dihedral : 7.596 83.476 5077 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.19 % Allowed : 15.24 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3258 helix: 0.30 (0.20), residues: 711 sheet: 0.35 (0.20), residues: 726 loop : -1.52 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B1092 TYR 0.019 0.001 TYR B1052 PHE 0.018 0.001 PHE B 227 TRP 0.007 0.001 TRP B 427 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00353 (27211) covalent geometry : angle 0.60234 (37028) SS BOND : bond 0.00624 ( 42) SS BOND : angle 1.78558 ( 84) hydrogen bonds : bond 0.04929 ( 882) hydrogen bonds : angle 5.29129 ( 2391) link_ALPHA1-2 : bond 0.00398 ( 1) link_ALPHA1-2 : angle 1.95948 ( 3) link_ALPHA1-3 : bond 0.03241 ( 3) link_ALPHA1-3 : angle 5.32431 ( 9) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.86664 ( 27) link_NAG-ASN : bond 0.00237 ( 57) link_NAG-ASN : angle 1.51427 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 0.757 Fit side-chains REVERT: A 688 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: A 894 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 935 ASP cc_start: 0.8296 (m-30) cc_final: 0.8029 (m-30) REVERT: A 995 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: A 1014 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8736 (tpp) REVERT: A 1071 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8447 (pttt) REVERT: B 271 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: B 296 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 424 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8967 (t) REVERT: C 315 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: C 616 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: C 761 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8205 (ttm170) REVERT: C 995 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7301 (mp10) outliers start: 91 outliers final: 41 residues processed: 245 average time/residue: 0.5979 time to fit residues: 170.4997 Evaluate side-chains 225 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1082 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1082 MET Chi-restraints excluded: chain C residue 1086 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 167 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 637 GLN B 192 ASN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.093010 restraints weight = 35550.777| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.39 r_work: 0.2799 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27323 Z= 0.155 Angle : 0.635 12.003 37322 Z= 0.313 Chirality : 0.046 0.282 4364 Planarity : 0.004 0.073 4692 Dihedral : 7.578 84.237 5077 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.52 % Allowed : 16.08 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3258 helix: 0.31 (0.20), residues: 708 sheet: 0.35 (0.20), residues: 726 loop : -1.55 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1092 TYR 0.020 0.001 TYR B1052 PHE 0.018 0.001 PHE B 227 TRP 0.007 0.001 TRP B 427 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00372 (27211) covalent geometry : angle 0.61454 (37028) SS BOND : bond 0.00650 ( 42) SS BOND : angle 1.87663 ( 84) hydrogen bonds : bond 0.04935 ( 882) hydrogen bonds : angle 5.27969 ( 2391) link_ALPHA1-2 : bond 0.00359 ( 1) link_ALPHA1-2 : angle 1.95235 ( 3) link_ALPHA1-3 : bond 0.03435 ( 3) link_ALPHA1-3 : angle 5.51606 ( 9) link_BETA1-4 : bond 0.00426 ( 9) link_BETA1-4 : angle 1.84204 ( 27) link_NAG-ASN : bond 0.00230 ( 57) link_NAG-ASN : angle 1.52838 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 177 time to evaluate : 1.070 Fit side-chains REVERT: A 435 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7479 (mmtp) REVERT: A 561 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7409 (p90) REVERT: A 688 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: A 690 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (pp) REVERT: A 894 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 935 ASP cc_start: 0.8260 (m-30) cc_final: 0.7988 (m-30) REVERT: A 995 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: A 1014 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8729 (tpp) REVERT: A 1071 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8448 (pttt) REVERT: B 271 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: B 296 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8764 (mm) REVERT: B 424 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8951 (t) REVERT: C 315 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 616 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: C 761 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (ttm170) REVERT: C 995 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7269 (mp10) outliers start: 72 outliers final: 41 residues processed: 228 average time/residue: 0.6822 time to fit residues: 180.0321 Evaluate side-chains 226 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 987 GLN Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 728 CYS Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1086 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 170 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 275 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 637 GLN B 192 ASN C 920 GLN C1086 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094750 restraints weight = 35254.427| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.35 r_work: 0.2832 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27323 Z= 0.122 Angle : 0.602 12.008 37322 Z= 0.296 Chirality : 0.045 0.270 4364 Planarity : 0.004 0.075 4692 Dihedral : 7.383 83.236 5077 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.86 % Allowed : 16.85 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3258 helix: 0.24 (0.20), residues: 735 sheet: 0.38 (0.20), residues: 729 loop : -1.57 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1092 TYR 0.018 0.001 TYR B1052 PHE 0.016 0.001 PHE B 227 TRP 0.008 0.001 TRP B 427 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00282 (27211) covalent geometry : angle 0.58203 (37028) SS BOND : bond 0.00542 ( 42) SS BOND : angle 1.65209 ( 84) hydrogen bonds : bond 0.04409 ( 882) hydrogen bonds : angle 5.19372 ( 2391) link_ALPHA1-2 : bond 0.00415 ( 1) link_ALPHA1-2 : angle 2.02512 ( 3) link_ALPHA1-3 : bond 0.03463 ( 3) link_ALPHA1-3 : angle 5.56916 ( 9) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 1.69318 ( 27) link_NAG-ASN : bond 0.00193 ( 57) link_NAG-ASN : angle 1.45741 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8608 (pp20) REVERT: A 894 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7263 (tp) REVERT: A 935 ASP cc_start: 0.8233 (m-30) cc_final: 0.7960 (m-30) REVERT: A 995 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: A 1014 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8699 (tpp) REVERT: A 1071 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8420 (pttt) REVERT: B 271 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: B 296 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 547 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8115 (mtmm) REVERT: B 557 ASP cc_start: 0.7927 (t0) cc_final: 0.7691 (t0) REVERT: C 315 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: C 616 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 761 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8084 (ttm170) outliers start: 53 outliers final: 29 residues processed: 224 average time/residue: 0.6469 time to fit residues: 167.8118 Evaluate side-chains 212 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 761 ARG Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 995 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 38 optimal weight: 0.0010 chunk 188 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 637 GLN B 192 ASN B1104 ASN C 789 GLN C1086 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094316 restraints weight = 35278.115| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.35 r_work: 0.2825 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27323 Z= 0.130 Angle : 0.612 12.000 37322 Z= 0.300 Chirality : 0.045 0.274 4364 Planarity : 0.004 0.076 4692 Dihedral : 7.344 83.245 5077 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 16.95 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3258 helix: 0.26 (0.20), residues: 732 sheet: 0.38 (0.20), residues: 720 loop : -1.57 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1092 TYR 0.017 0.001 TYR B1052 PHE 0.017 0.001 PHE B 227 TRP 0.007 0.001 TRP B 427 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00303 (27211) covalent geometry : angle 0.59209 (37028) SS BOND : bond 0.00564 ( 42) SS BOND : angle 1.65065 ( 84) hydrogen bonds : bond 0.04505 ( 882) hydrogen bonds : angle 5.18059 ( 2391) link_ALPHA1-2 : bond 0.00371 ( 1) link_ALPHA1-2 : angle 1.98036 ( 3) link_ALPHA1-3 : bond 0.03534 ( 3) link_ALPHA1-3 : angle 5.68435 ( 9) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 1.71036 ( 27) link_NAG-ASN : bond 0.00203 ( 57) link_NAG-ASN : angle 1.46879 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8656.05 seconds wall clock time: 148 minutes 21.49 seconds (8901.49 seconds total)