Starting phenix.real_space_refine on Sun Jun 22 23:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy0_60551/06_2025/8zy0_60551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy0_60551/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy0_60551/06_2025/8zy0_60551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy0_60551/06_2025/8zy0_60551.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy0_60551/06_2025/8zy0_60551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy0_60551/06_2025/8zy0_60551.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.59, per 1000 atoms: 0.59 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: 6.20 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.67 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: 12.05 Time building geometry restraints manager: 7.45 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 1126 or resid 1201 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 1126 or resid 1201 through 1216 \ )) selection = (chain 'C' and (resid 17 through 1126 or resid 1201 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: 0.910 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.060 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (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 TRP 0.007 0.001 TRP B 622 HIS 0.006 0.001 HIS C 169 PHE 0.035 0.001 PHE B1106 TYR 0.018 0.001 TYR B 484 ARG 0.004 0.000 ARG B 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 57) link_NAG-ASN : angle 1.65635 ( 171) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 1.98431 ( 27) 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) hydrogen bonds : bond 0.23861 ( 882) hydrogen bonds : angle 8.29862 ( 2391) SS BOND : bond 0.00752 ( 42) SS BOND : angle 1.75970 ( 84) covalent geometry : bond 0.00472 (27211) covalent geometry : angle 0.74399 (37028) *********************** 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 : 3.040 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: 1.3421 time to fit residues: 501.3768 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 : 2.829 ------------------------------------------------------------------------------- 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 276 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 256 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 304 GLN C 617 GLN C 920 GLN C1091 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094223 restraints weight = 35403.106| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.40 r_work: 0.2859 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27323 Z= 0.174 Angle : 0.656 9.738 37322 Z= 0.328 Chirality : 0.047 0.282 4364 Planarity : 0.004 0.055 4692 Dihedral : 10.565 103.480 5079 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.65 % Allowed : 8.65 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3258 helix: -0.60 (0.19), residues: 732 sheet: 0.41 (0.20), residues: 738 loop : -1.83 (0.12), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 427 HIS 0.004 0.001 HIS B 188 PHE 0.030 0.002 PHE A 337 TYR 0.024 0.001 TYR B1052 ARG 0.013 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 57) link_NAG-ASN : angle 1.57818 ( 171) link_BETA1-4 : bond 0.00641 ( 9) link_BETA1-4 : angle 2.10425 ( 27) link_ALPHA1-2 : bond 0.00613 ( 1) link_ALPHA1-2 : angle 1.98527 ( 3) link_ALPHA1-3 : bond 0.02602 ( 3) link_ALPHA1-3 : angle 4.28492 ( 9) hydrogen bonds : bond 0.05710 ( 882) hydrogen bonds : angle 6.01022 ( 2391) SS BOND : bond 0.00591 ( 42) SS BOND : angle 1.71667 ( 84) covalent geometry : bond 0.00411 (27211) covalent geometry : angle 0.63800 (37028) *********************** 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 254 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 2.933 Fit side-chains revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8395 (p) cc_final: 0.8115 (m) REVERT: A 557 ASP cc_start: 0.8115 (t70) cc_final: 0.7906 (t0) REVERT: A 765 ASP cc_start: 0.8566 (m-30) cc_final: 0.8352 (m-30) REVERT: A 935 ASP cc_start: 0.8210 (m-30) cc_final: 0.7947 (m-30) REVERT: A 995 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: B 45 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7222 (p0) REVERT: B 914 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7957 (m110) REVERT: B 1071 LYS cc_start: 0.8363 (pttm) cc_final: 0.8107 (pttp) REVERT: B 1115 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 271 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: C 761 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8211 (ttm170) REVERT: C 1115 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8452 (mm) outliers start: 47 outliers final: 13 residues processed: 237 average time/residue: 1.5747 time to fit residues: 433.8412 Evaluate side-chains 198 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 914 ASN 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 688 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 156 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN A 910 ASN A 934 GLN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091986 restraints weight = 35295.097| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.38 r_work: 0.2807 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27323 Z= 0.195 Angle : 0.670 11.291 37322 Z= 0.335 Chirality : 0.048 0.296 4364 Planarity : 0.004 0.042 4692 Dihedral : 9.421 95.021 5077 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.77 % Allowed : 11.07 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3258 helix: -0.26 (0.20), residues: 705 sheet: 0.32 (0.20), residues: 732 loop : -1.70 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.005 0.001 HIS C 188 PHE 0.025 0.002 PHE A 337 TYR 0.022 0.001 TYR B1052 ARG 0.015 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 57) link_NAG-ASN : angle 1.64076 ( 171) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 2.15365 ( 27) link_ALPHA1-2 : bond 0.00548 ( 1) link_ALPHA1-2 : angle 1.82718 ( 3) link_ALPHA1-3 : bond 0.02717 ( 3) link_ALPHA1-3 : angle 4.73090 ( 9) hydrogen bonds : bond 0.05953 ( 882) hydrogen bonds : angle 5.70097 ( 2391) SS BOND : bond 0.00639 ( 42) SS BOND : angle 1.82627 ( 84) covalent geometry : bond 0.00475 (27211) covalent geometry : angle 0.65081 (37028) *********************** 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 281 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 3.075 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7365 (pp) REVERT: A 208 VAL cc_start: 0.8424 (p) cc_final: 0.8112 (m) REVERT: A 557 ASP cc_start: 0.8070 (t70) cc_final: 0.7840 (t0) REVERT: A 765 ASP cc_start: 0.8603 (m-30) cc_final: 0.8341 (m-30) REVERT: A 935 ASP cc_start: 0.8323 (m-30) cc_final: 0.8058 (m-30) REVERT: B 45 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7322 (p0) REVERT: B 296 LEU cc_start: 0.8998 (mm) cc_final: 0.8770 (mm) REVERT: B 637 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8061 (tm-30) REVERT: B 854 MET cc_start: 0.8974 (mtp) cc_final: 0.8674 (mtp) REVERT: B 1115 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 271 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: C 315 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: C 547 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8537 (mmmt) REVERT: C 616 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: C 761 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8334 (ttm170) REVERT: C 885 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8871 (mtm) REVERT: C 1115 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8682 (mm) outliers start: 79 outliers final: 28 residues processed: 261 average time/residue: 1.3664 time to fit residues: 417.0186 Evaluate side-chains 211 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 79 LEU 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 432 VAL Chi-restraints excluded: chain A residue 558 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 45 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 1108 SER Chi-restraints excluded: chain B residue 1115 ILE 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 315 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 730 ASP 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 296 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 911 GLN B 934 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 = 0.3444 r_free = 0.3444 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094780 restraints weight = 35678.105| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.37 r_work: 0.2847 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27323 Z= 0.111 Angle : 0.582 11.258 37322 Z= 0.287 Chirality : 0.045 0.275 4364 Planarity : 0.004 0.053 4692 Dihedral : 8.590 90.855 5077 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.59 % Allowed : 13.17 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3258 helix: 0.05 (0.20), residues: 711 sheet: 0.41 (0.20), residues: 735 loop : -1.63 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 427 HIS 0.002 0.001 HIS A 188 PHE 0.018 0.001 PHE C1106 TYR 0.018 0.001 TYR B1052 ARG 0.011 0.000 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 57) link_NAG-ASN : angle 1.46597 ( 171) link_BETA1-4 : bond 0.00459 ( 9) link_BETA1-4 : angle 1.96777 ( 27) link_ALPHA1-2 : bond 0.00691 ( 1) link_ALPHA1-2 : angle 2.19602 ( 3) link_ALPHA1-3 : bond 0.02897 ( 3) link_ALPHA1-3 : angle 4.73458 ( 9) hydrogen bonds : bond 0.04608 ( 882) hydrogen bonds : angle 5.47798 ( 2391) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.35176 ( 84) covalent geometry : bond 0.00244 (27211) covalent geometry : angle 0.56467 (37028) *********************** 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 283 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 209 time to evaluate : 4.641 Fit side-chains REVERT: A 208 VAL cc_start: 0.8421 (p) cc_final: 0.8207 (m) REVERT: A 268 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: A 935 ASP cc_start: 0.8292 (m-30) cc_final: 0.8000 (m-30) REVERT: A 995 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: B 296 LEU cc_start: 0.8980 (mm) cc_final: 0.8753 (mm) REVERT: B 424 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8936 (t) REVERT: B 547 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8187 (mtmm) REVERT: B 637 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8026 (tm-30) REVERT: B 854 MET cc_start: 0.8948 (mtp) cc_final: 0.8646 (mtp) REVERT: B 1115 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8790 (mm) REVERT: C 271 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: C 547 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8551 (mmmt) REVERT: C 761 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8169 (ttm170) REVERT: C 885 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8845 (mtm) REVERT: C 995 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7304 (mp10) outliers start: 74 outliers final: 26 residues processed: 263 average time/residue: 1.3742 time to fit residues: 425.7053 Evaluate side-chains 214 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 2.735 ------------------------------------------------------------------------------- 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 268 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 995 GLN 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 424 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 739 LEU 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 271 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 468 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 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 135 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 307 ASN A 617 GLN A1104 ASN B1043 HIS B1104 ASN C 841 ASN C 920 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.087758 restraints weight = 35768.090| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.37 r_work: 0.2698 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 27323 Z= 0.343 Angle : 0.838 15.425 37322 Z= 0.418 Chirality : 0.055 0.326 4364 Planarity : 0.005 0.056 4692 Dihedral : 9.131 96.355 5077 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.73 % Allowed : 13.56 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3258 helix: -0.50 (0.19), residues: 711 sheet: 0.34 (0.20), residues: 708 loop : -1.82 (0.12), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 427 HIS 0.007 0.002 HIS A 201 PHE 0.027 0.003 PHE B 227 TYR 0.025 0.002 TYR B1052 ARG 0.012 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 57) link_NAG-ASN : angle 1.99762 ( 171) link_BETA1-4 : bond 0.00424 ( 9) link_BETA1-4 : angle 2.49634 ( 27) link_ALPHA1-2 : bond 0.00319 ( 1) link_ALPHA1-2 : angle 1.81476 ( 3) link_ALPHA1-3 : bond 0.02693 ( 3) link_ALPHA1-3 : angle 5.12048 ( 9) hydrogen bonds : bond 0.07227 ( 882) hydrogen bonds : angle 5.79257 ( 2391) SS BOND : bond 0.01176 ( 42) SS BOND : angle 2.76624 ( 84) covalent geometry : bond 0.00856 (27211) covalent geometry : angle 0.81243 (37028) *********************** 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 322 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 187 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 79 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7226 (pp) REVERT: A 82 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: A 268 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: A 435 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7635 (mmtp) REVERT: A 935 ASP cc_start: 0.8449 (m-30) cc_final: 0.8149 (m-30) REVERT: A 995 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: B 296 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 637 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8090 (tm-30) REVERT: B 765 ASP cc_start: 0.8916 (m-30) cc_final: 0.8589 (m-30) REVERT: B 899 ASN cc_start: 0.8651 (t0) cc_final: 0.8419 (t0) REVERT: C 271 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7047 (pp20) REVERT: C 315 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: C 547 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8548 (mmmt) REVERT: C 616 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 761 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8189 (ttm170) REVERT: C 935 ASP cc_start: 0.8434 (m-30) cc_final: 0.8133 (m-30) REVERT: C 975 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: C 995 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: C 1115 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8830 (mm) outliers start: 135 outliers final: 62 residues processed: 291 average time/residue: 1.2222 time to fit residues: 423.5783 Evaluate side-chains 251 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 79 LEU 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 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 432 VAL 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 633 MET Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 995 GLN 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 265 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 640 CYS Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 763 THR 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 B residue 1108 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 540 VAL 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 618 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 688 GLN Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 716 MET 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 896 VAL Chi-restraints excluded: chain C residue 975 GLU Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1053 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 61 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN B 617 GLN C 439 ASN C 553 GLN C 789 GLN C 920 GLN C1086 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090000 restraints weight = 35481.441| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.37 r_work: 0.2769 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27323 Z= 0.181 Angle : 0.682 11.818 37322 Z= 0.339 Chirality : 0.048 0.294 4364 Planarity : 0.004 0.058 4692 Dihedral : 8.646 94.510 5077 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.75 % Allowed : 15.27 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3258 helix: -0.35 (0.19), residues: 735 sheet: 0.39 (0.20), residues: 708 loop : -1.84 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 427 HIS 0.004 0.001 HIS C 201 PHE 0.019 0.001 PHE B 227 TYR 0.021 0.001 TYR A 494 ARG 0.014 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 57) link_NAG-ASN : angle 1.74725 ( 171) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 2.07811 ( 27) link_ALPHA1-2 : bond 0.00532 ( 1) link_ALPHA1-2 : angle 2.05670 ( 3) link_ALPHA1-3 : bond 0.02907 ( 3) link_ALPHA1-3 : angle 4.91039 ( 9) hydrogen bonds : bond 0.05614 ( 882) hydrogen bonds : angle 5.56645 ( 2391) SS BOND : bond 0.00701 ( 42) SS BOND : angle 2.30646 ( 84) covalent geometry : bond 0.00436 (27211) covalent geometry : angle 0.65789 (37028) *********************** 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 297 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 190 time to evaluate : 4.410 Fit side-chains REVERT: A 82 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 268 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 435 LYS cc_start: 0.8122 (ptpt) cc_final: 0.7677 (mmtp) REVERT: A 557 ASP cc_start: 0.8093 (t0) cc_final: 0.7827 (t0) REVERT: A 561 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7269 (p90) REVERT: A 688 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: A 710 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: A 894 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7484 (tp) REVERT: A 935 ASP cc_start: 0.8415 (m-30) cc_final: 0.8112 (m-30) REVERT: A 995 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: B 547 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8209 (mtmm) REVERT: B 637 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8034 (tm-30) REVERT: B 765 ASP cc_start: 0.8845 (m-30) cc_final: 0.8520 (m-30) REVERT: B 799 TYR cc_start: 0.7694 (m-10) cc_final: 0.7388 (p90) REVERT: B 854 MET cc_start: 0.9002 (mtp) cc_final: 0.8786 (mtp) REVERT: C 45 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7230 (p0) REVERT: C 271 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: C 547 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8540 (mmmt) REVERT: C 616 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: C 761 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7992 (ttm170) REVERT: C 935 ASP cc_start: 0.8444 (m-30) cc_final: 0.8129 (m-30) REVERT: C 975 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 995 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 107 outliers final: 46 residues processed: 267 average time/residue: 1.5827 time to fit residues: 498.1937 Evaluate side-chains 234 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 VAL 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 386 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 561 PHE 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 710 GLU 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 1081 VAL Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 323 THR 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 640 CYS Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 948 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 45 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 552 GLN 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 688 GLN 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 975 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 60 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 159 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 56 optimal weight: 0.0570 overall best weight: 0.8218 ------------------------------------------------------------------------------- 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 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 = 0.3420 r_free = 0.3420 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093124 restraints weight = 35394.300| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.38 r_work: 0.2789 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2259 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= 0.117 Angle : 0.611 11.924 37322 Z= 0.302 Chirality : 0.045 0.273 4364 Planarity : 0.004 0.064 4692 Dihedral : 8.172 91.144 5077 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.87 % Allowed : 16.18 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3258 helix: -0.01 (0.20), residues: 738 sheet: 0.43 (0.20), residues: 702 loop : -1.76 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1087 HIS 0.015 0.001 HIS C1086 PHE 0.016 0.001 PHE B 227 TYR 0.018 0.001 TYR B1052 ARG 0.016 0.000 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 57) link_NAG-ASN : angle 1.58853 ( 171) link_BETA1-4 : bond 0.00433 ( 9) link_BETA1-4 : angle 1.84575 ( 27) link_ALPHA1-2 : bond 0.00564 ( 1) link_ALPHA1-2 : angle 2.14491 ( 3) link_ALPHA1-3 : bond 0.03141 ( 3) link_ALPHA1-3 : angle 4.91584 ( 9) hydrogen bonds : bond 0.04616 ( 882) hydrogen bonds : angle 5.36584 ( 2391) SS BOND : bond 0.00522 ( 42) SS BOND : angle 1.85176 ( 84) covalent geometry : bond 0.00259 (27211) covalent geometry : angle 0.58973 (37028) *********************** 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 275 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 193 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: A 265 MET cc_start: 0.9115 (mmm) cc_final: 0.8771 (mmm) REVERT: A 268 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: A 315 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: A 557 ASP cc_start: 0.7933 (t0) cc_final: 0.7692 (t0) REVERT: A 688 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: A 710 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 894 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7291 (tp) REVERT: A 935 ASP cc_start: 0.8344 (m-30) cc_final: 0.8026 (m-30) REVERT: A 995 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: B 424 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8973 (t) REVERT: B 547 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8145 (mtmm) REVERT: B 637 GLN cc_start: 0.8727 (mm-40) cc_final: 0.7984 (tm-30) REVERT: B 765 ASP cc_start: 0.8727 (m-30) cc_final: 0.8362 (m-30) REVERT: B 854 MET cc_start: 0.8996 (mtp) cc_final: 0.8686 (mtp) REVERT: C 547 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8521 (mmmt) REVERT: C 616 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 761 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8138 (ttm170) REVERT: C 935 ASP cc_start: 0.8370 (m-30) cc_final: 0.8055 (m-30) REVERT: C 995 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: C 1115 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8741 (mm) outliers start: 82 outliers final: 42 residues processed: 254 average time/residue: 1.3321 time to fit residues: 397.9610 Evaluate side-chains 233 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 323 THR 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 710 GLU 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 896 VAL Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1035 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 205 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 776 THR 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 82 PHE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 540 VAL 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 618 VAL Chi-restraints excluded: chain C residue 640 CYS 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 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 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 284 optimal weight: 0.7980 chunk 217 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 150 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 0.0980 chunk 304 optimal weight: 0.0270 chunk 207 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 274 optimal weight: 0.0050 overall best weight: 0.2030 ------------------------------------------------------------------------------- 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 A1086 HIS B 192 ASN B1104 ASN C 789 GLN C 920 GLN C1086 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097223 restraints weight = 35644.205| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.38 r_work: 0.2903 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27323 Z= 0.097 Angle : 0.557 11.811 37322 Z= 0.274 Chirality : 0.044 0.258 4364 Planarity : 0.003 0.064 4692 Dihedral : 7.545 86.391 5077 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.21 % Allowed : 17.44 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3258 helix: 0.36 (0.20), residues: 732 sheet: 0.55 (0.20), residues: 699 loop : -1.70 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.005 0.000 HIS C1086 PHE 0.015 0.001 PHE B 227 TYR 0.016 0.001 TYR C1052 ARG 0.018 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 57) link_NAG-ASN : angle 1.37674 ( 171) link_BETA1-4 : bond 0.00471 ( 9) link_BETA1-4 : angle 1.54799 ( 27) link_ALPHA1-2 : bond 0.00498 ( 1) link_ALPHA1-2 : angle 2.10508 ( 3) link_ALPHA1-3 : bond 0.03241 ( 3) link_ALPHA1-3 : angle 5.00533 ( 9) hydrogen bonds : bond 0.03544 ( 882) hydrogen bonds : angle 5.08524 ( 2391) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.31433 ( 84) covalent geometry : bond 0.00201 (27211) covalent geometry : angle 0.54019 (37028) *********************** 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 278 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: A 299 GLU cc_start: 0.8552 (mp0) cc_final: 0.8344 (mm-30) REVERT: A 475 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7692 (tm) REVERT: A 688 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 935 ASP cc_start: 0.8310 (m-30) cc_final: 0.7988 (m-30) REVERT: B 271 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7371 (pp20) REVERT: B 547 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8113 (mtmm) REVERT: B 557 ASP cc_start: 0.7891 (t0) cc_final: 0.7666 (t0) REVERT: B 637 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8062 (tm-30) REVERT: B 854 MET cc_start: 0.8990 (mtp) cc_final: 0.8726 (mtp) REVERT: C 328 PHE cc_start: 0.7218 (m-80) cc_final: 0.7018 (m-80) REVERT: C 547 LYS cc_start: 0.8818 (mmtm) cc_final: 0.8522 (mmmt) REVERT: C 761 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8012 (ttm170) REVERT: C 935 ASP cc_start: 0.8356 (m-30) cc_final: 0.8043 (m-30) REVERT: C 995 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7394 (mp10) outliers start: 63 outliers final: 25 residues processed: 262 average time/residue: 1.2951 time to fit residues: 399.1086 Evaluate side-chains 224 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 558 VAL 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 711 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 776 THR 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 323 THR Chi-restraints excluded: chain C residue 640 CYS 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 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 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 268 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 chunk 158 optimal weight: 0.4980 chunk 292 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 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 192 ASN B1104 ASN C 789 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094945 restraints weight = 35562.967| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.36 r_work: 0.2828 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2297 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= 0.119 Angle : 0.588 11.877 37322 Z= 0.290 Chirality : 0.045 0.269 4364 Planarity : 0.004 0.071 4692 Dihedral : 7.532 87.580 5077 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.03 % Allowed : 18.07 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3258 helix: 0.41 (0.20), residues: 729 sheet: 0.46 (0.20), residues: 714 loop : -1.63 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1087 HIS 0.013 0.001 HIS C1086 PHE 0.018 0.001 PHE B 227 TYR 0.017 0.001 TYR B 581 ARG 0.016 0.000 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 57) link_NAG-ASN : angle 1.40006 ( 171) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 1.67538 ( 27) link_ALPHA1-2 : bond 0.00469 ( 1) link_ALPHA1-2 : angle 2.09351 ( 3) link_ALPHA1-3 : bond 0.03299 ( 3) link_ALPHA1-3 : angle 5.14712 ( 9) hydrogen bonds : bond 0.04064 ( 882) hydrogen bonds : angle 5.07888 ( 2391) SS BOND : bond 0.00598 ( 42) SS BOND : angle 1.54094 ( 84) covalent geometry : bond 0.00274 (27211) covalent geometry : angle 0.57062 (37028) *********************** 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 245 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 299 GLU cc_start: 0.8542 (mp0) cc_final: 0.8327 (mm-30) REVERT: A 688 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: A 935 ASP cc_start: 0.8301 (m-30) cc_final: 0.7988 (m-30) REVERT: A 1014 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8392 (tpp) REVERT: B 271 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: B 296 LEU cc_start: 0.8965 (mm) cc_final: 0.8740 (mm) REVERT: B 557 ASP cc_start: 0.7914 (t0) cc_final: 0.7683 (t0) REVERT: B 637 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8035 (tm-30) REVERT: B 854 MET cc_start: 0.9011 (mtp) cc_final: 0.8703 (mtp) REVERT: C 547 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8506 (mmmt) REVERT: C 761 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: C 935 ASP cc_start: 0.8346 (m-30) cc_final: 0.8032 (m-30) REVERT: C 995 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7368 (mp10) outliers start: 58 outliers final: 33 residues processed: 230 average time/residue: 1.5409 time to fit residues: 418.6173 Evaluate side-chains 217 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 558 VAL 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 711 VAL Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 896 VAL 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 144 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 776 THR 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 82 PHE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 640 CYS Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 728 CYS 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 269 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 254 optimal weight: 0.3980 chunk 238 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 231 optimal weight: 0.4980 chunk 179 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 250 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 192 ASN A 637 GLN B1104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094311 restraints weight = 35417.551| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.39 r_work: 0.2822 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27323 Z= 0.131 Angle : 0.609 11.982 37322 Z= 0.299 Chirality : 0.045 0.273 4364 Planarity : 0.004 0.076 4692 Dihedral : 7.551 88.319 5077 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 18.39 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3258 helix: 0.45 (0.20), residues: 729 sheet: 0.44 (0.20), residues: 714 loop : -1.65 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.003 0.001 HIS C 188 PHE 0.018 0.001 PHE B 227 TYR 0.017 0.001 TYR B 581 ARG 0.018 0.001 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 57) link_NAG-ASN : angle 1.43832 ( 171) link_BETA1-4 : bond 0.00400 ( 9) link_BETA1-4 : angle 1.71567 ( 27) link_ALPHA1-2 : bond 0.00425 ( 1) link_ALPHA1-2 : angle 1.97582 ( 3) link_ALPHA1-3 : bond 0.03295 ( 3) link_ALPHA1-3 : angle 5.18945 ( 9) hydrogen bonds : bond 0.04343 ( 882) hydrogen bonds : angle 5.12021 ( 2391) SS BOND : bond 0.00529 ( 42) SS BOND : angle 1.64451 ( 84) covalent geometry : bond 0.00307 (27211) covalent geometry : angle 0.59048 (37028) ********************** 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 234 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: A 315 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8656 (tm-30) REVERT: A 475 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7747 (tm) REVERT: A 688 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: A 935 ASP cc_start: 0.8316 (m-30) cc_final: 0.8010 (m-30) REVERT: A 975 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 995 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: A 1014 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8427 (tpp) REVERT: B 271 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7369 (pp20) REVERT: B 296 LEU cc_start: 0.8968 (mm) cc_final: 0.8749 (mm) REVERT: B 547 LYS cc_start: 0.8512 (mmmt) cc_final: 0.7996 (mtmm) REVERT: B 557 ASP cc_start: 0.7930 (t0) cc_final: 0.7692 (t0) REVERT: B 854 MET cc_start: 0.8994 (mtp) cc_final: 0.8660 (mtp) REVERT: C 547 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8512 (mmmt) REVERT: C 761 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8080 (ttm170) REVERT: C 935 ASP cc_start: 0.8375 (m-30) cc_final: 0.8066 (m-30) REVERT: C 995 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7294 (mp10) outliers start: 53 outliers final: 34 residues processed: 218 average time/residue: 1.4526 time to fit residues: 368.8487 Evaluate side-chains 222 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 475 LEU 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 733 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 975 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 144 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 995 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 82 PHE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 552 GLN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 640 CYS 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 728 CYS 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 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B1104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095390 restraints weight = 35436.134| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.36 r_work: 0.2832 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27323 Z= 0.110 Angle : 0.587 11.727 37322 Z= 0.288 Chirality : 0.044 0.265 4364 Planarity : 0.004 0.075 4692 Dihedral : 7.409 87.801 5077 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.79 % Allowed : 18.53 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3258 helix: 0.54 (0.21), residues: 714 sheet: 0.43 (0.19), residues: 729 loop : -1.65 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.002 0.001 HIS C 188 PHE 0.016 0.001 PHE B 227 TYR 0.018 0.001 TYR B 581 ARG 0.018 0.000 ARG B1092 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 57) link_NAG-ASN : angle 1.41719 ( 171) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 1.64254 ( 27) link_ALPHA1-2 : bond 0.00463 ( 1) link_ALPHA1-2 : angle 1.97610 ( 3) link_ALPHA1-3 : bond 0.03186 ( 3) link_ALPHA1-3 : angle 5.15685 ( 9) hydrogen bonds : bond 0.04074 ( 882) hydrogen bonds : angle 5.09686 ( 2391) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.49970 ( 84) covalent geometry : bond 0.00249 (27211) covalent geometry : angle 0.56939 (37028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18693.09 seconds wall clock time: 327 minutes 46.34 seconds (19666.34 seconds total)