Starting phenix.real_space_refine on Sat Mar 7 06:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hca_34657/03_2026/8hca_34657.map" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4818 atoms to isotropic. 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 156 5.16 5 C 22344 2.51 5 N 5802 2.21 5 O 6885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35187 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.25, per 1000 atoms: 0.23 Number of scatterers: 35187 At special positions: 0 Unit cell: (161.7, 150.15, 244.2, 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 156 16.00 O 6885 8.00 N 5802 7.00 C 22344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 111 " - pdb=" SG CYS F 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 217 " 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8322 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 73 sheets defined 19.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.827A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.851A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.605A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.558A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.928A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.984A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.104A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.836A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.304A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.126A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.005A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.209A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.551A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.780A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.823A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.544A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.623A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.844A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.693A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 188 through 193 removed outlier: 4.303A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.669A pdb=" N THR F 31 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.098A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.156A pdb=" N VAL G 88 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.311A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.969A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.071A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.654A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.826A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.155A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.738A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.634A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.828A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.183A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.751A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.820A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.391A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.712A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.441A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.734A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.679A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.991A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.225A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.792A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.524A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.067A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.878A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.656A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.555A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 398 through 403 removed outlier: 3.710A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.182A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'E' and resid 49 through 53 removed outlier: 6.815A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.665A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.705A pdb=" N TRP E 153 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 212 " --> pdb=" O CYS E 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.619A pdb=" N PHE F 84 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 35 through 38 removed outlier: 5.782A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 50 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR F 63 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.807A pdb=" N GLY F 160 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 158 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER F 201 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 199 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 165 " --> pdb=" O TYR F 197 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR F 197 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.637A pdb=" N THR F 172 " --> pdb=" O ASN F 220 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR F 215 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.719A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.952A pdb=" N ILE L 21 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 49 through 53 removed outlier: 4.080A pdb=" N LEU L 52 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.598A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.542A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 48 through 53 removed outlier: 6.472A pdb=" N LYS G 44 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 51 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU G 42 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 39 " --> pdb=" O MET G 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 67 through 70 Processing sheet with id=AG8, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.821A pdb=" N ASN G 143 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.741A pdb=" N TRP G 153 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.850A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 86 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.588A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 172 through 175 removed outlier: 4.942A pdb=" N TYR H 215 " --> pdb=" O VAL H 232 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.801A pdb=" N GLY D 10 " --> pdb=" O ILE D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.528A pdb=" N PHE D 84 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 141 through 148 removed outlier: 4.084A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 202 " --> pdb=" O HIS D 185 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.565A pdb=" N VAL D 219 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 228 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 3093 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: 8.77 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11196 1.34 - 1.46: 8829 1.46 - 1.58: 15765 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 35985 Sorted by residual: bond pdb=" C ARG A 328 " pdb=" N PHE A 329 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.69e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C GLU H 169 " pdb=" N PRO H 170 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 48069 1.98 - 3.96: 794 3.96 - 5.95: 91 5.95 - 7.93: 23 7.93 - 9.91: 7 Bond angle restraints: 48984 Sorted by residual: angle pdb=" CA PHE D 167 " pdb=" C PHE D 167 " pdb=" N PRO D 168 " ideal model delta sigma weight residual 120.58 117.63 2.95 7.40e-01 1.83e+00 1.59e+01 angle pdb=" C PRO C 987 " pdb=" N GLU C 988 " pdb=" CA GLU C 988 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ARG A 328 " pdb=" CA ARG A 328 " pdb=" C ARG A 328 " ideal model delta sigma weight residual 109.31 114.61 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" C ILE C 587 " pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 121.80 130.52 -8.72 2.44e+00 1.68e-01 1.28e+01 angle pdb=" C ARG A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta sigma weight residual 122.77 118.22 4.55 1.33e+00 5.65e-01 1.17e+01 ... (remaining 48979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 20010 17.54 - 35.09: 1767 35.09 - 52.63: 337 52.63 - 70.18: 75 70.18 - 87.72: 41 Dihedral angle restraints: 22230 sinusoidal: 9294 harmonic: 12936 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.40 84.60 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.17 84.17 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 22227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5189 0.085 - 0.170: 521 0.170 - 0.255: 7 0.255 - 0.340: 2 0.340 - 0.425: 5 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 5721 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG A1305 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 205 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO D 206 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 206 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 206 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 330 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.035 5.00e-02 4.00e+02 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6508 2.78 - 3.31: 30990 3.31 - 3.84: 57877 3.84 - 4.37: 62979 4.37 - 4.90: 110752 Nonbonded interactions: 269106 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.250 3.040 nonbonded pdb=" O CYS A1032 " pdb=" OG SER A1051 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.270 3.040 ... (remaining 269101 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.690 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.003 0.070 36096 Z= 0.160 Angle : 0.616 15.624 49260 Z= 0.298 Chirality : 0.047 0.425 5724 Planarity : 0.004 0.070 6255 Dihedral : 13.561 87.722 13737 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.44 % Allowed : 0.34 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4383 helix: 1.21 (0.20), residues: 657 sheet: 1.04 (0.17), residues: 960 loop : -1.31 (0.11), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 106 TYR 0.008 0.001 TYR G 54 PHE 0.013 0.001 PHE A 541 TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (35985) covalent geometry : angle 0.59517 (48984) SS BOND : bond 0.00165 ( 57) SS BOND : angle 0.58407 ( 114) hydrogen bonds : bond 0.22861 ( 1099) hydrogen bonds : angle 8.56367 ( 3093) link_BETA1-4 : bond 0.00452 ( 12) link_BETA1-4 : angle 0.86916 ( 36) link_NAG-ASN : bond 0.00708 ( 42) link_NAG-ASN : angle 3.19313 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.4652 (mtmm) REVERT: A 302 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 332 ILE cc_start: 0.8102 (pt) cc_final: 0.7630 (tp) REVERT: A 1050 MET cc_start: 0.8700 (pmm) cc_final: 0.8413 (pmm) REVERT: B 1050 MET cc_start: 0.8171 (pmm) cc_final: 0.7705 (pmm) REVERT: C 424 LYS cc_start: 0.8170 (tttt) cc_final: 0.7967 (ttmm) REVERT: E 192 GLU cc_start: 0.0092 (mm-30) cc_final: -0.0483 (pt0) REVERT: F 129 MET cc_start: 0.5922 (tpp) cc_final: 0.4545 (tpp) REVERT: L 170 GLU cc_start: 0.4642 (tp30) cc_final: 0.4157 (tt0) REVERT: G 40 TRP cc_start: 0.5618 (m100) cc_final: 0.5148 (m100) outliers start: 17 outliers final: 3 residues processed: 169 average time/residue: 0.2158 time to fit residues: 61.5592 Evaluate side-chains 100 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 0.2980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.0770 overall best weight: 1.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 907 ASN B 804 GLN C 188 ASN E 165 GLN F 33 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.054685 restraints weight = 266335.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.054303 restraints weight = 191930.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.053976 restraints weight = 150535.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054165 restraints weight = 142074.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054173 restraints weight = 127703.120| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36096 Z= 0.111 Angle : 0.527 13.115 49260 Z= 0.263 Chirality : 0.044 0.410 5724 Planarity : 0.004 0.062 6255 Dihedral : 5.823 59.818 5904 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4383 helix: 1.92 (0.21), residues: 676 sheet: 1.02 (0.16), residues: 1038 loop : -1.16 (0.12), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.016 0.001 TYR D 197 PHE 0.016 0.001 PHE C 275 TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00238 (35985) covalent geometry : angle 0.50755 (48984) SS BOND : bond 0.00617 ( 57) SS BOND : angle 0.77987 ( 114) hydrogen bonds : bond 0.03891 ( 1099) hydrogen bonds : angle 6.14299 ( 3093) link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.20574 ( 36) link_NAG-ASN : bond 0.00549 ( 42) link_NAG-ASN : angle 2.69678 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7772 (pt) cc_final: 0.7252 (tp) REVERT: A 740 MET cc_start: 0.8338 (tpt) cc_final: 0.7892 (tpt) REVERT: A 1050 MET cc_start: 0.8816 (pmm) cc_final: 0.8462 (pmm) REVERT: B 869 MET cc_start: 0.8512 (pmm) cc_final: 0.8292 (pmm) REVERT: B 1050 MET cc_start: 0.8261 (pmm) cc_final: 0.7767 (pmm) REVERT: E 154 LYS cc_start: 0.5420 (mppt) cc_final: 0.3737 (ptmm) REVERT: E 192 GLU cc_start: 0.0315 (mm-30) cc_final: -0.0276 (pt0) REVERT: F 33 ASN cc_start: 0.6867 (m-40) cc_final: 0.5995 (m-40) REVERT: F 129 MET cc_start: 0.6008 (tpp) cc_final: 0.4723 (tpp) REVERT: L 94 MET cc_start: -0.1884 (mmt) cc_final: -0.2415 (tpp) REVERT: L 170 GLU cc_start: 0.4832 (tp30) cc_final: 0.4390 (tt0) REVERT: G 94 MET cc_start: -0.0538 (ptp) cc_final: -0.0833 (ptp) REVERT: D 34 MET cc_start: 0.2181 (tpt) cc_final: 0.1871 (mmm) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.2151 time to fit residues: 49.7632 Evaluate side-chains 90 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 176 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 28 optimal weight: 0.0000 chunk 250 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 382 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 overall best weight: 3.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 448 ASN A1011 GLN A1071 GLN A1083 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 417 ASN B 613 GLN B1036 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 HIS H 192 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.071330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.052692 restraints weight = 283035.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051414 restraints weight = 221368.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.051370 restraints weight = 192072.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.051480 restraints weight = 166613.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051537 restraints weight = 147125.700| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36096 Z= 0.208 Angle : 0.662 12.703 49260 Z= 0.332 Chirality : 0.046 0.397 5724 Planarity : 0.006 0.245 6255 Dihedral : 5.956 58.490 5904 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4383 helix: 1.72 (0.20), residues: 667 sheet: 0.84 (0.16), residues: 1068 loop : -1.25 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.024 0.002 TYR A 313 PHE 0.028 0.002 PHE C 55 TRP 0.031 0.002 TRP A 64 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00449 (35985) covalent geometry : angle 0.64202 (48984) SS BOND : bond 0.00475 ( 57) SS BOND : angle 1.40120 ( 114) hydrogen bonds : bond 0.04143 ( 1099) hydrogen bonds : angle 5.71835 ( 3093) link_BETA1-4 : bond 0.00219 ( 12) link_BETA1-4 : angle 1.59137 ( 36) link_NAG-ASN : bond 0.00706 ( 42) link_NAG-ASN : angle 2.92452 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.5953 (p) cc_final: 0.5673 (t) REVERT: A 332 ILE cc_start: 0.8024 (pt) cc_final: 0.7518 (tp) REVERT: A 697 MET cc_start: 0.6555 (tpt) cc_final: 0.6324 (tpt) REVERT: A 731 MET cc_start: 0.8751 (ptp) cc_final: 0.8475 (ptm) REVERT: A 740 MET cc_start: 0.8611 (tpt) cc_final: 0.8245 (tpt) REVERT: A 1050 MET cc_start: 0.8890 (pmm) cc_final: 0.8657 (pmm) REVERT: B 1050 MET cc_start: 0.8506 (pmm) cc_final: 0.7500 (pmm) REVERT: C 455 LEU cc_start: 0.7900 (tt) cc_final: 0.7576 (tt) REVERT: C 869 MET cc_start: 0.8557 (pmm) cc_final: 0.7999 (pmm) REVERT: C 900 MET cc_start: 0.8659 (ppp) cc_final: 0.8229 (ppp) REVERT: E 17 GLU cc_start: 0.4649 (pp20) cc_final: 0.3895 (pm20) REVERT: E 154 LYS cc_start: 0.4326 (mppt) cc_final: 0.2521 (pttp) REVERT: E 192 GLU cc_start: 0.0572 (mm-30) cc_final: 0.0204 (pt0) REVERT: F 87 MET cc_start: 0.3802 (tpt) cc_final: 0.3548 (tpt) REVERT: G 94 MET cc_start: -0.1424 (ptp) cc_final: -0.1888 (ptp) REVERT: D 34 MET cc_start: 0.3795 (tpt) cc_final: 0.2479 (mmm) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 0.2231 time to fit residues: 48.3464 Evaluate side-chains 82 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 438 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 388 optimal weight: 8.9990 chunk 391 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 237 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 404 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN A 607 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1071 GLN A1135 ASN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN C 437 ASN C 481 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN D 126 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.070501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.051829 restraints weight = 280832.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.050604 restraints weight = 212580.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050527 restraints weight = 184982.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.050587 restraints weight = 160634.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.050693 restraints weight = 142502.773| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36096 Z= 0.183 Angle : 0.607 13.054 49260 Z= 0.304 Chirality : 0.046 0.425 5724 Planarity : 0.004 0.059 6255 Dihedral : 5.746 59.685 5904 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4383 helix: 1.63 (0.20), residues: 675 sheet: 0.68 (0.16), residues: 1090 loop : -1.29 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 905 TYR 0.024 0.002 TYR C 508 PHE 0.028 0.002 PHE A 541 TRP 0.024 0.001 TRP B 353 HIS 0.013 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00396 (35985) covalent geometry : angle 0.58749 (48984) SS BOND : bond 0.00352 ( 57) SS BOND : angle 1.17934 ( 114) hydrogen bonds : bond 0.03695 ( 1099) hydrogen bonds : angle 5.52788 ( 3093) link_BETA1-4 : bond 0.00227 ( 12) link_BETA1-4 : angle 1.21788 ( 36) link_NAG-ASN : bond 0.00604 ( 42) link_NAG-ASN : angle 2.82210 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8775 (tpt) cc_final: 0.8401 (tpt) REVERT: A 1050 MET cc_start: 0.8879 (pmm) cc_final: 0.8656 (pmm) REVERT: B 455 LEU cc_start: 0.7652 (tp) cc_final: 0.7171 (tp) REVERT: B 1050 MET cc_start: 0.8328 (pmm) cc_final: 0.7275 (pmm) REVERT: C 869 MET cc_start: 0.8487 (pmm) cc_final: 0.8159 (pmm) REVERT: C 900 MET cc_start: 0.8663 (ppp) cc_final: 0.8151 (ppp) REVERT: E 17 GLU cc_start: 0.5035 (pp20) cc_final: 0.4490 (pm20) REVERT: E 154 LYS cc_start: 0.4336 (mppt) cc_final: 0.2311 (ptmm) REVERT: E 192 GLU cc_start: 0.0597 (mm-30) cc_final: 0.0214 (pt0) REVERT: F 129 MET cc_start: 0.6426 (tpp) cc_final: 0.5399 (tpp) REVERT: G 94 MET cc_start: -0.0794 (ptp) cc_final: -0.1118 (ptp) REVERT: H 78 ASP cc_start: 0.6372 (m-30) cc_final: 0.5927 (m-30) REVERT: D 34 MET cc_start: 0.4227 (tpt) cc_final: 0.2838 (tpp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2150 time to fit residues: 41.3373 Evaluate side-chains 82 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 30 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 283 optimal weight: 0.0270 chunk 277 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 404 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 99 ASN A 218 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 448 ASN C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.069177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.050149 restraints weight = 267267.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048686 restraints weight = 203268.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048804 restraints weight = 155484.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.049031 restraints weight = 132630.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049081 restraints weight = 117133.508| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36096 Z= 0.193 Angle : 0.630 13.101 49260 Z= 0.313 Chirality : 0.046 0.431 5724 Planarity : 0.005 0.109 6255 Dihedral : 5.865 57.471 5904 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.73 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4383 helix: 1.46 (0.20), residues: 680 sheet: 0.58 (0.16), residues: 1079 loop : -1.35 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 408 TYR 0.019 0.002 TYR A 369 PHE 0.025 0.002 PHE A 541 TRP 0.031 0.002 TRP B 353 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00417 (35985) covalent geometry : angle 0.60876 (48984) SS BOND : bond 0.00384 ( 57) SS BOND : angle 1.34225 ( 114) hydrogen bonds : bond 0.03781 ( 1099) hydrogen bonds : angle 5.53095 ( 3093) link_BETA1-4 : bond 0.00262 ( 12) link_BETA1-4 : angle 1.37138 ( 36) link_NAG-ASN : bond 0.00562 ( 42) link_NAG-ASN : angle 2.95094 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8128 (m) cc_final: 0.7889 (p) REVERT: A 552 LEU cc_start: 0.4467 (tt) cc_final: 0.3811 (mp) REVERT: A 740 MET cc_start: 0.8749 (tpt) cc_final: 0.8371 (tpt) REVERT: B 1050 MET cc_start: 0.8353 (pmm) cc_final: 0.7426 (pmm) REVERT: C 869 MET cc_start: 0.8201 (pmm) cc_final: 0.7557 (pmm) REVERT: C 900 MET cc_start: 0.8724 (ppp) cc_final: 0.8150 (ppp) REVERT: E 17 GLU cc_start: 0.5363 (pp20) cc_final: 0.4689 (pm20) REVERT: E 65 ASP cc_start: 0.7156 (t0) cc_final: 0.6793 (t0) REVERT: E 154 LYS cc_start: 0.4381 (mppt) cc_final: 0.2718 (pttp) REVERT: E 192 GLU cc_start: 0.0459 (mm-30) cc_final: 0.0144 (pt0) REVERT: F 129 MET cc_start: 0.6369 (tpp) cc_final: 0.4956 (tpp) REVERT: L 121 PHE cc_start: 0.4900 (m-10) cc_final: 0.3853 (t80) REVERT: D 34 MET cc_start: 0.4181 (tpt) cc_final: 0.3096 (tpp) outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.2280 time to fit residues: 43.7889 Evaluate side-chains 85 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 150 optimal weight: 0.0270 chunk 201 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 329 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 99 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 239 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.069832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.050602 restraints weight = 275462.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.049385 restraints weight = 195076.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049529 restraints weight = 162677.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049487 restraints weight = 162410.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049600 restraints weight = 130574.663| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36096 Z= 0.140 Angle : 0.584 17.361 49260 Z= 0.287 Chirality : 0.045 0.425 5724 Planarity : 0.004 0.058 6255 Dihedral : 5.601 57.481 5904 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 4383 helix: 1.64 (0.20), residues: 681 sheet: 0.56 (0.16), residues: 1052 loop : -1.32 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 408 TYR 0.011 0.001 TYR B 873 PHE 0.024 0.001 PHE A 541 TRP 0.015 0.001 TRP G 40 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (35985) covalent geometry : angle 0.56237 (48984) SS BOND : bond 0.00325 ( 57) SS BOND : angle 1.08157 ( 114) hydrogen bonds : bond 0.03482 ( 1099) hydrogen bonds : angle 5.36116 ( 3093) link_BETA1-4 : bond 0.00275 ( 12) link_BETA1-4 : angle 1.15581 ( 36) link_NAG-ASN : bond 0.00538 ( 42) link_NAG-ASN : angle 3.00007 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8268 (m) cc_final: 0.7988 (p) REVERT: A 697 MET cc_start: 0.7654 (mmp) cc_final: 0.7299 (mmm) REVERT: A 740 MET cc_start: 0.8948 (tpt) cc_final: 0.8561 (tpt) REVERT: A 780 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 1050 MET cc_start: 0.8889 (pmm) cc_final: 0.8665 (pmm) REVERT: B 1050 MET cc_start: 0.8348 (pmm) cc_final: 0.7242 (pmm) REVERT: C 869 MET cc_start: 0.8209 (pmm) cc_final: 0.7949 (pmm) REVERT: C 900 MET cc_start: 0.8811 (ppp) cc_final: 0.8190 (ppp) REVERT: C 1029 MET cc_start: 0.8754 (tpp) cc_final: 0.8508 (tpp) REVERT: E 17 GLU cc_start: 0.5312 (pp20) cc_final: 0.4685 (pm20) REVERT: E 154 LYS cc_start: 0.4181 (mppt) cc_final: 0.2422 (ptmm) REVERT: E 192 GLU cc_start: -0.0096 (mm-30) cc_final: -0.0318 (pt0) REVERT: F 129 MET cc_start: 0.6269 (tpp) cc_final: 0.4868 (tpp) REVERT: L 121 PHE cc_start: 0.4831 (m-10) cc_final: 0.3782 (t80) REVERT: L 128 GLU cc_start: 0.3942 (pp20) cc_final: 0.3595 (pp20) REVERT: H 104 ARG cc_start: 0.6114 (tmt-80) cc_final: 0.5846 (ttp80) REVERT: D 34 MET cc_start: 0.5043 (tpt) cc_final: 0.3650 (tpp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2214 time to fit residues: 40.5027 Evaluate side-chains 84 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 71 optimal weight: 5.9990 chunk 427 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 419 optimal weight: 8.9990 chunk 391 optimal weight: 0.0770 chunk 354 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.069960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.050648 restraints weight = 274293.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.049116 restraints weight = 201164.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049486 restraints weight = 179737.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049348 restraints weight = 164276.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049515 restraints weight = 132551.345| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36096 Z= 0.120 Angle : 0.559 12.001 49260 Z= 0.276 Chirality : 0.044 0.419 5724 Planarity : 0.004 0.058 6255 Dihedral : 5.372 56.447 5904 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4383 helix: 1.79 (0.20), residues: 681 sheet: 0.57 (0.16), residues: 1113 loop : -1.26 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.020 0.001 TYR B 369 PHE 0.022 0.001 PHE A 541 TRP 0.016 0.001 TRP B 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (35985) covalent geometry : angle 0.53798 (48984) SS BOND : bond 0.00284 ( 57) SS BOND : angle 1.03210 ( 114) hydrogen bonds : bond 0.03384 ( 1099) hydrogen bonds : angle 5.24962 ( 3093) link_BETA1-4 : bond 0.00228 ( 12) link_BETA1-4 : angle 1.12412 ( 36) link_NAG-ASN : bond 0.00532 ( 42) link_NAG-ASN : angle 2.88553 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.4465 (tt) cc_final: 0.3317 (mp) REVERT: A 697 MET cc_start: 0.7597 (mmp) cc_final: 0.7287 (mmm) REVERT: A 740 MET cc_start: 0.8944 (tpt) cc_final: 0.8539 (tpt) REVERT: A 1050 MET cc_start: 0.8976 (pmm) cc_final: 0.8730 (pmm) REVERT: B 1050 MET cc_start: 0.8253 (pmm) cc_final: 0.7226 (pmm) REVERT: C 869 MET cc_start: 0.8268 (pmm) cc_final: 0.7983 (pmm) REVERT: C 900 MET cc_start: 0.8529 (ppp) cc_final: 0.7826 (ppp) REVERT: C 1029 MET cc_start: 0.8639 (tpp) cc_final: 0.8080 (tpt) REVERT: E 17 GLU cc_start: 0.5382 (pp20) cc_final: 0.4822 (pm20) REVERT: E 154 LYS cc_start: 0.4154 (mppt) cc_final: 0.2583 (pttp) REVERT: F 129 MET cc_start: 0.6248 (tpp) cc_final: 0.4827 (tpp) REVERT: L 128 GLU cc_start: 0.3913 (pp20) cc_final: 0.3536 (pp20) REVERT: G 40 TRP cc_start: 0.7065 (m100) cc_final: 0.6157 (m100) REVERT: D 34 MET cc_start: 0.4530 (tpt) cc_final: 0.3689 (tpp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2080 time to fit residues: 38.0875 Evaluate side-chains 77 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 134 optimal weight: 0.5980 chunk 320 optimal weight: 4.9990 chunk 199 optimal weight: 0.0170 chunk 279 optimal weight: 0.7980 chunk 371 optimal weight: 30.0000 chunk 406 optimal weight: 0.6980 chunk 378 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 675 GLN C 901 GLN C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.050840 restraints weight = 275672.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049542 restraints weight = 197632.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.049871 restraints weight = 164412.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049771 restraints weight = 147572.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.049875 restraints weight = 134722.264| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36096 Z= 0.105 Angle : 0.547 14.121 49260 Z= 0.269 Chirality : 0.044 0.408 5724 Planarity : 0.004 0.057 6255 Dihedral : 5.190 55.852 5904 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4383 helix: 1.89 (0.20), residues: 681 sheet: 0.61 (0.16), residues: 1110 loop : -1.21 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.015 0.001 TYR B 369 PHE 0.019 0.001 PHE A 541 TRP 0.014 0.001 TRP G 40 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00233 (35985) covalent geometry : angle 0.52661 (48984) SS BOND : bond 0.00259 ( 57) SS BOND : angle 0.97498 ( 114) hydrogen bonds : bond 0.03274 ( 1099) hydrogen bonds : angle 5.10656 ( 3093) link_BETA1-4 : bond 0.00256 ( 12) link_BETA1-4 : angle 1.00917 ( 36) link_NAG-ASN : bond 0.00528 ( 42) link_NAG-ASN : angle 2.79917 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.3590 (tt) cc_final: 0.2448 (mp) REVERT: A 740 MET cc_start: 0.8910 (tpt) cc_final: 0.8511 (tpt) REVERT: A 1050 MET cc_start: 0.9003 (pmm) cc_final: 0.8728 (pmm) REVERT: B 675 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7472 (pp30) REVERT: B 1050 MET cc_start: 0.8245 (pmm) cc_final: 0.7154 (pmm) REVERT: C 869 MET cc_start: 0.8267 (pmm) cc_final: 0.7935 (pmm) REVERT: C 900 MET cc_start: 0.8536 (ppp) cc_final: 0.8018 (ppp) REVERT: E 17 GLU cc_start: 0.5294 (pp20) cc_final: 0.4986 (pm20) REVERT: E 67 PHE cc_start: 0.1870 (m-10) cc_final: 0.1061 (m-10) REVERT: E 148 GLU cc_start: 0.5226 (pm20) cc_final: 0.4982 (pm20) REVERT: E 154 LYS cc_start: 0.4137 (mppt) cc_final: 0.2456 (ptmm) REVERT: F 129 MET cc_start: 0.6198 (tpp) cc_final: 0.4858 (tpp) REVERT: L 128 GLU cc_start: 0.3980 (pp20) cc_final: 0.3614 (pp20) REVERT: G 40 TRP cc_start: 0.7011 (m100) cc_final: 0.5978 (m100) REVERT: H 149 SER cc_start: 0.4470 (m) cc_final: 0.4263 (t) REVERT: D 34 MET cc_start: 0.4554 (tpt) cc_final: 0.2722 (mmm) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2166 time to fit residues: 39.5322 Evaluate side-chains 84 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 216 optimal weight: 30.0000 chunk 324 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 293 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 427 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.069230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.050646 restraints weight = 276712.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.049418 restraints weight = 212258.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.049456 restraints weight = 165245.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049527 restraints weight = 148428.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049581 restraints weight = 135841.673| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36096 Z= 0.159 Angle : 0.594 14.346 49260 Z= 0.295 Chirality : 0.045 0.472 5724 Planarity : 0.004 0.057 6255 Dihedral : 5.473 58.094 5904 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4383 helix: 1.80 (0.20), residues: 675 sheet: 0.47 (0.16), residues: 1111 loop : -1.25 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.018 0.001 TYR B 369 PHE 0.023 0.001 PHE A 541 TRP 0.018 0.001 TRP H 36 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (35985) covalent geometry : angle 0.57336 (48984) SS BOND : bond 0.00335 ( 57) SS BOND : angle 1.15361 ( 114) hydrogen bonds : bond 0.03508 ( 1099) hydrogen bonds : angle 5.24449 ( 3093) link_BETA1-4 : bond 0.00141 ( 12) link_BETA1-4 : angle 1.30296 ( 36) link_NAG-ASN : bond 0.00534 ( 42) link_NAG-ASN : angle 2.91485 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.4920 (tt) cc_final: 0.3881 (mp) REVERT: A 740 MET cc_start: 0.8902 (tpt) cc_final: 0.8584 (tpt) REVERT: A 1050 MET cc_start: 0.9000 (pmm) cc_final: 0.8660 (pmm) REVERT: B 1050 MET cc_start: 0.8434 (pmm) cc_final: 0.7269 (pmm) REVERT: C 869 MET cc_start: 0.8325 (pmm) cc_final: 0.7966 (pmm) REVERT: C 900 MET cc_start: 0.8608 (ppp) cc_final: 0.7924 (ppp) REVERT: C 1029 MET cc_start: 0.9015 (tpp) cc_final: 0.8441 (tpt) REVERT: E 17 GLU cc_start: 0.5517 (pp20) cc_final: 0.5274 (pm20) REVERT: E 148 GLU cc_start: 0.5417 (pm20) cc_final: 0.5180 (pm20) REVERT: E 154 LYS cc_start: 0.4285 (mppt) cc_final: 0.2614 (pttp) REVERT: F 129 MET cc_start: 0.5762 (tpp) cc_final: 0.4427 (tpp) REVERT: F 167 PHE cc_start: 0.3447 (t80) cc_final: 0.2750 (t80) REVERT: L 128 GLU cc_start: 0.3659 (pp20) cc_final: 0.3327 (pp20) REVERT: L 192 GLU cc_start: 0.5724 (mm-30) cc_final: 0.5201 (tt0) REVERT: G 40 TRP cc_start: 0.7091 (m100) cc_final: 0.6215 (m100) REVERT: H 149 SER cc_start: 0.4746 (m) cc_final: 0.4519 (t) REVERT: D 34 MET cc_start: 0.4607 (tpt) cc_final: 0.2440 (mmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2169 time to fit residues: 39.1475 Evaluate side-chains 82 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 126 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 17 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 171 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.068468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048533 restraints weight = 281521.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048039 restraints weight = 184835.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047700 restraints weight = 156298.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047820 restraints weight = 144547.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.048067 restraints weight = 115111.363| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36096 Z= 0.185 Angle : 0.634 11.642 49260 Z= 0.316 Chirality : 0.046 0.475 5724 Planarity : 0.005 0.119 6255 Dihedral : 5.827 57.008 5904 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 4383 helix: 1.62 (0.20), residues: 672 sheet: 0.26 (0.16), residues: 1062 loop : -1.35 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 905 TYR 0.018 0.001 TYR B 369 PHE 0.025 0.002 PHE A 541 TRP 0.014 0.001 TRP B 353 HIS 0.014 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00405 (35985) covalent geometry : angle 0.61304 (48984) SS BOND : bond 0.00453 ( 57) SS BOND : angle 1.42005 ( 114) hydrogen bonds : bond 0.03729 ( 1099) hydrogen bonds : angle 5.44479 ( 3093) link_BETA1-4 : bond 0.00202 ( 12) link_BETA1-4 : angle 1.32728 ( 36) link_NAG-ASN : bond 0.00543 ( 42) link_NAG-ASN : angle 2.98313 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.5086 (tt) cc_final: 0.3832 (mp) REVERT: A 740 MET cc_start: 0.8945 (tpt) cc_final: 0.8601 (tpt) REVERT: A 780 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 1050 MET cc_start: 0.8959 (pmm) cc_final: 0.8577 (pmm) REVERT: B 1050 MET cc_start: 0.8243 (pmm) cc_final: 0.7460 (pmm) REVERT: C 869 MET cc_start: 0.8415 (pmm) cc_final: 0.8026 (pmm) REVERT: C 900 MET cc_start: 0.8756 (ppp) cc_final: 0.8000 (ppp) REVERT: C 1029 MET cc_start: 0.9015 (tpp) cc_final: 0.8395 (tpt) REVERT: E 17 GLU cc_start: 0.6027 (pp20) cc_final: 0.5780 (pm20) REVERT: E 113 ARG cc_start: 0.7699 (mmp-170) cc_final: 0.6362 (ppt170) REVERT: E 148 GLU cc_start: 0.5358 (pm20) cc_final: 0.5158 (pm20) REVERT: E 154 LYS cc_start: 0.4327 (mppt) cc_final: 0.2680 (pttp) REVERT: F 129 MET cc_start: 0.5587 (tpp) cc_final: 0.4180 (tpp) REVERT: L 94 MET cc_start: 0.1072 (tpp) cc_final: 0.0693 (tpp) REVERT: L 192 GLU cc_start: 0.5759 (mm-30) cc_final: 0.5314 (tt0) REVERT: G 6 GLN cc_start: 0.3283 (OUTLIER) cc_final: 0.2492 (pt0) REVERT: G 40 TRP cc_start: 0.7610 (m100) cc_final: 0.6860 (m100) REVERT: H 149 SER cc_start: 0.4579 (m) cc_final: 0.4338 (t) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.2269 time to fit residues: 41.8443 Evaluate side-chains 89 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 50 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 425 optimal weight: 1.9990 chunk 331 optimal weight: 30.0000 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048898 restraints weight = 280640.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048180 restraints weight = 203818.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048034 restraints weight = 150607.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048116 restraints weight = 154031.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.048533 restraints weight = 119399.867| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36096 Z= 0.137 Angle : 0.585 10.971 49260 Z= 0.291 Chirality : 0.045 0.478 5724 Planarity : 0.004 0.057 6255 Dihedral : 5.527 57.014 5904 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4383 helix: 1.75 (0.20), residues: 673 sheet: 0.32 (0.16), residues: 1079 loop : -1.33 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.016 0.001 TYR B 369 PHE 0.032 0.001 PHE A 329 TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (35985) covalent geometry : angle 0.56410 (48984) SS BOND : bond 0.00339 ( 57) SS BOND : angle 1.29681 ( 114) hydrogen bonds : bond 0.03540 ( 1099) hydrogen bonds : angle 5.29487 ( 3093) link_BETA1-4 : bond 0.00223 ( 12) link_BETA1-4 : angle 1.15648 ( 36) link_NAG-ASN : bond 0.00512 ( 42) link_NAG-ASN : angle 2.88397 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.32 seconds wall clock time: 94 minutes 42.77 seconds (5682.77 seconds total)